Starting phenix.real_space_refine on Tue Aug 4 12:24:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/21bq_67558/08_2026/21bq_67558.cif Found real_map, /net/cci-nas-00/data/ceres_data/21bq_67558/08_2026/21bq_67558.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/21bq_67558/08_2026/21bq_67558.map" default_real_map = "/net/cci-nas-00/data/ceres_data/21bq_67558/08_2026/21bq_67558.map" model { file = "/net/cci-nas-00/data/ceres_data/21bq_67558/08_2026/21bq_67558.cif" } default_model = "/net/cci-nas-00/data/ceres_data/21bq_67558/08_2026/21bq_67558.cif" } resolution = 2.7 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= 0.011 sd= 0.215 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: 3 Type Number sf(0) Gaussians C 1540 2.51 5 N 480 2.21 5 O 560 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 2580 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 516 Unusual residues: {'ACE': 1} Classifications: {'peptide': 63, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'PTRANS': 1, 'TRANS': 61} Restraints were copied for chains: B, C, D, E Residues with excluded nonbonded symmetry interactions: 5 residue: pdb=" C ACE A 1 " occ=0.00 pdb=" O ACE A 1 " occ=0.00 pdb=" CH3 ACE A 1 " occ=0.00 residue: pdb=" C ACE B 1 " occ=0.00 pdb=" O ACE B 1 " occ=0.00 pdb=" CH3 ACE B 1 " occ=0.00 residue: pdb=" C ACE C 1 " occ=0.00 pdb=" O ACE C 1 " occ=0.00 pdb=" CH3 ACE C 1 " occ=0.00 residue: pdb=" C ACE D 1 " occ=0.00 pdb=" O ACE D 1 " occ=0.00 pdb=" CH3 ACE D 1 " occ=0.00 residue: pdb=" C ACE E 1 " occ=0.00 pdb=" O ACE E 1 " occ=0.00 pdb=" CH3 ACE E 1 " occ=0.00 Time building chain proxies: 0.37, per 1000 atoms: 0.14 Number of scatterers: 2580 At special positions: 0 Unit cell: (59.547, 69.903, 40.1295, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 560 8.00 N 480 7.00 C 1540 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 0.13 Conformation dependent library (CDL) restraints added in 53.6 milliseconds 610 Ramachandran restraints generated. 305 Oldfield, 0 Emsley, 305 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 530 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 6 sheets defined 0.0% alpha, 33.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.05 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 8 through 16 Processing sheet with id=AA2, first strand: chain 'A' and resid 22 through 24 removed outlier: 6.481A pdb=" N GLN A 23 " --> pdb=" O GLN B 24 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N GLN B 23 " --> pdb=" O GLN C 24 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N GLN C 23 " --> pdb=" O GLN D 24 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N GLN D 23 " --> pdb=" O GLN E 24 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 28 through 29 Processing sheet with id=AA4, first strand: chain 'A' and resid 35 through 39 removed outlier: 5.861A pdb=" N TYR A 35 " --> pdb=" O ASN B 36 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N GLN B 38 " --> pdb=" O TYR A 35 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N ALA A 37 " --> pdb=" O GLN B 38 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N TYR B 35 " --> pdb=" O ASN C 36 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N GLN C 38 " --> pdb=" O TYR B 35 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ALA B 37 " --> pdb=" O GLN C 38 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N TYR C 35 " --> pdb=" O ASN D 36 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N GLN D 38 " --> pdb=" O TYR C 35 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ALA C 37 " --> pdb=" O GLN D 38 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N TYR D 35 " --> pdb=" O ASN E 36 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N GLN E 38 " --> pdb=" O TYR D 35 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ALA D 37 " --> pdb=" O GLN E 38 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 45 through 49 Processing sheet with id=AA6, first strand: chain 'A' and resid 61 through 63 removed outlier: 6.444A pdb=" N GLN A 61 " --> pdb=" O GLN B 62 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N GLN B 61 " --> pdb=" O GLN C 62 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N GLN C 61 " --> pdb=" O GLN D 62 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N GLN D 61 " --> pdb=" O GLN E 62 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 52 hydrogen bonds defined for protein. 156 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: 0.22 Time building geometry restraints manager: 0.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.28: 480 1.28 - 1.35: 480 1.35 - 1.41: 420 1.41 - 1.47: 345 1.47 - 1.53: 915 Bond restraints: 2640 Sorted by residual: bond pdb=" C ACE B 1 " pdb=" O ACE B 1 " ideal model delta sigma weight residual 1.199 1.231 -0.032 2.00e-02 2.50e+03 2.53e+00 bond pdb=" C ACE D 1 " pdb=" O ACE D 1 " ideal model delta sigma weight residual 1.199 1.230 -0.031 2.00e-02 2.50e+03 2.41e+00 bond pdb=" C ACE E 1 " pdb=" O ACE E 1 " ideal model delta sigma weight residual 1.199 1.230 -0.031 2.00e-02 2.50e+03 2.39e+00 bond pdb=" C ACE A 1 " pdb=" O ACE A 1 " ideal model delta sigma weight residual 1.199 1.230 -0.031 2.00e-02 2.50e+03 2.35e+00 bond pdb=" C ACE C 1 " pdb=" O ACE C 1 " ideal model delta sigma weight residual 1.199 1.230 -0.031 2.00e-02 2.50e+03 2.33e+00 ... (remaining 2635 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.75: 3172 0.75 - 1.50: 309 1.50 - 2.25: 72 2.25 - 3.00: 4 3.00 - 3.76: 8 Bond angle restraints: 3565 Sorted by residual: angle pdb=" CA GLY B 59 " pdb=" C GLY B 59 " pdb=" N TYR B 60 " ideal model delta sigma weight residual 115.43 117.52 -2.09 1.18e+00 7.18e-01 3.15e+00 angle pdb=" CA GLY A 59 " pdb=" C GLY A 59 " pdb=" N TYR A 60 " ideal model delta sigma weight residual 115.43 117.50 -2.07 1.18e+00 7.18e-01 3.07e+00 angle pdb=" CA GLY E 59 " pdb=" C GLY E 59 " pdb=" N TYR E 60 " ideal model delta sigma weight residual 115.43 117.46 -2.03 1.18e+00 7.18e-01 2.97e+00 angle pdb=" CA GLY D 59 " pdb=" C GLY D 59 " pdb=" N TYR D 60 " ideal model delta sigma weight residual 115.43 117.45 -2.02 1.18e+00 7.18e-01 2.93e+00 angle pdb=" CA GLY C 59 " pdb=" C GLY C 59 " pdb=" N TYR C 60 " ideal model delta sigma weight residual 115.43 117.44 -2.01 1.18e+00 7.18e-01 2.90e+00 ... (remaining 3560 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.03: 1265 13.03 - 26.06: 140 26.06 - 39.09: 50 39.09 - 52.12: 35 52.12 - 65.15: 5 Dihedral angle restraints: 1495 sinusoidal: 595 harmonic: 900 Sorted by residual: dihedral pdb=" CA ARG A 28 " pdb=" CB ARG A 28 " pdb=" CG ARG A 28 " pdb=" CD ARG A 28 " ideal model delta sinusoidal sigma weight residual -60.00 -102.55 42.55 3 1.50e+01 4.44e-03 7.64e+00 dihedral pdb=" CA ARG E 28 " pdb=" CB ARG E 28 " pdb=" CG ARG E 28 " pdb=" CD ARG E 28 " ideal model delta sinusoidal sigma weight residual -60.00 -102.50 42.50 3 1.50e+01 4.44e-03 7.63e+00 dihedral pdb=" CA ARG C 28 " pdb=" CB ARG C 28 " pdb=" CG ARG C 28 " pdb=" CD ARG C 28 " ideal model delta sinusoidal sigma weight residual -60.00 -102.50 42.50 3 1.50e+01 4.44e-03 7.63e+00 ... (remaining 1492 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.018: 102 0.018 - 0.036: 73 0.036 - 0.054: 61 0.054 - 0.072: 23 0.072 - 0.090: 6 Chirality restraints: 265 Sorted by residual: chirality pdb=" CA TYR E 60 " pdb=" N TYR E 60 " pdb=" C TYR E 60 " pdb=" CB TYR E 60 " both_signs ideal model delta sigma weight residual False 2.51 2.42 0.09 2.00e-01 2.50e+01 2.03e-01 chirality pdb=" CA TYR D 60 " pdb=" N TYR D 60 " pdb=" C TYR D 60 " pdb=" CB TYR D 60 " both_signs ideal model delta sigma weight residual False 2.51 2.42 0.09 2.00e-01 2.50e+01 2.00e-01 chirality pdb=" CA TYR B 60 " pdb=" N TYR B 60 " pdb=" C TYR B 60 " pdb=" CB TYR B 60 " both_signs ideal model delta sigma weight residual False 2.51 2.42 0.09 2.00e-01 2.50e+01 1.99e-01 ... (remaining 262 not shown) Planarity restraints: 540 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR D 60 " -0.006 2.00e-02 2.50e+03 6.02e-03 7.24e-01 pdb=" CG TYR D 60 " 0.015 2.00e-02 2.50e+03 pdb=" CD1 TYR D 60 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 TYR D 60 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR D 60 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR D 60 " -0.003 2.00e-02 2.50e+03 pdb=" CZ TYR D 60 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR D 60 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 60 " -0.006 2.00e-02 2.50e+03 6.00e-03 7.21e-01 pdb=" CG TYR A 60 " 0.015 2.00e-02 2.50e+03 pdb=" CD1 TYR A 60 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 TYR A 60 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR A 60 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR A 60 " -0.003 2.00e-02 2.50e+03 pdb=" CZ TYR A 60 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR A 60 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 60 " -0.007 2.00e-02 2.50e+03 5.98e-03 7.14e-01 pdb=" CG TYR E 60 " 0.015 2.00e-02 2.50e+03 pdb=" CD1 TYR E 60 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 TYR E 60 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR E 60 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR E 60 " -0.003 2.00e-02 2.50e+03 pdb=" CZ TYR E 60 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR E 60 " -0.001 2.00e-02 2.50e+03 ... (remaining 537 not shown) Histogram of nonbonded interaction distances: 2.62 - 3.08: 1832 3.08 - 3.53: 2721 3.53 - 3.99: 4999 3.99 - 4.44: 5907 4.44 - 4.90: 10345 Nonbonded interactions: 25804 Sorted by model distance: nonbonded pdb=" N SER D 17 " pdb=" O SER D 17 " model vdw 2.623 2.496 nonbonded pdb=" N SER C 17 " pdb=" O SER C 17 " model vdw 2.624 2.496 nonbonded pdb=" N SER A 17 " pdb=" O SER A 17 " model vdw 2.624 2.496 nonbonded pdb=" N SER E 17 " pdb=" O SER E 17 " model vdw 2.624 2.496 nonbonded pdb=" N SER B 17 " pdb=" O SER B 17 " model vdw 2.624 2.496 ... (remaining 25799 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 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } 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=0.00 max=1.00 mean=0.99 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: 1.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.020 Check model and map are aligned: 0.010 Set scattering table: 0.000 Process input model: 2.620 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.000 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:5.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 2640 Z= 0.260 Angle : 0.507 3.755 3565 Z= 0.317 Chirality : 0.035 0.090 265 Planarity : 0.002 0.015 540 Dihedral : 14.895 65.149 965 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.04 % Allowed : 8.16 % Favored : 89.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -3.77 (0.23), residues: 305 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.87 (0.18), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG B 28 TYR 0.015 0.002 TYR A 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00523 / 0.26 ( 2640) covalent geometry : angle 0.50712 / 0.32 ( 3565) hydrogen bonds : bond 0.09158 / 6.03 ( 52) hydrogen bonds : angle 5.74252 / 4.07 ( 156) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 610 Ramachandran restraints generated. 305 Oldfield, 0 Emsley, 305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 610 Ramachandran restraints generated. 305 Oldfield, 0 Emsley, 305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 34 time to evaluate : 0.057 Fit side-chains REVERT: A 6 GLN cc_start: 0.8375 (OUTLIER) cc_final: 0.7497 (mp10) REVERT: A 47 GLN cc_start: 0.9098 (tt0) cc_final: 0.8843 (tt0) REVERT: B 5 ASN cc_start: 0.8283 (t0) cc_final: 0.7929 (t0) REVERT: B 6 GLN cc_start: 0.8266 (OUTLIER) cc_final: 0.7740 (mp10) REVERT: B 60 TYR cc_start: 0.8096 (p90) cc_final: 0.7841 (p90) REVERT: C 9 ASN cc_start: 0.8790 (t0) cc_final: 0.8478 (t0) REVERT: D 6 GLN cc_start: 0.8256 (OUTLIER) cc_final: 0.7509 (mp10) REVERT: E 6 GLN cc_start: 0.8522 (OUTLIER) cc_final: 0.8088 (mp10) REVERT: E 21 ASN cc_start: 0.9143 (m-40) cc_final: 0.8835 (m-40) REVERT: E 48 ASN cc_start: 0.9374 (t0) cc_final: 0.9067 (t0) outliers start: 5 outliers final: 0 residues processed: 38 average time/residue: 0.2638 time to fit residues: 10.3716 Evaluate side-chains 26 residues out of total 245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 22 time to evaluate : 0.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 GLN Chi-restraints excluded: chain B residue 6 GLN Chi-restraints excluded: chain D residue 6 GLN Chi-restraints excluded: chain E residue 6 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 27 optimal weight: 3.9990 chunk 12 optimal weight: 5.9990 chunk 24 optimal weight: 8.9990 chunk 28 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 16 optimal weight: 0.0770 chunk 15 optimal weight: 1.9990 chunk 29 optimal weight: 0.2980 chunk 25 optimal weight: 0.6980 overall best weight: 0.5940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 21 ASN B 23 GLN B 27 ASN B 48 ASN C 8 ASN ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 21 ASN C 23 GLN C 27 ASN C 48 ASN ** D 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 23 GLN D 27 ASN D 48 ASN ** E 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 23 GLN E 27 ASN E 48 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.110487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.089608 restraints weight = 3439.543| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 1.95 r_work: 0.3421 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3318 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.1165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.010 2640 Z= 0.108 Angle : 0.404 3.982 3565 Z= 0.230 Chirality : 0.034 0.076 265 Planarity : 0.002 0.015 540 Dihedral : 7.547 48.507 397 Min Nonbonded Distance : 2.638 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % Rotamer: Outliers : 2.45 % Allowed : 14.69 % Favored : 82.86 % 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 are not related in a simple way. whole: -3.78 (0.25), residues: 305 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.87 (0.19), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 28 TYR 0.021 0.001 TYR C 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.11 ( 2640) covalent geometry : angle 0.40406 / 0.23 ( 3565) hydrogen bonds : bond 0.02450 / 1.59 ( 52) hydrogen bonds : angle 3.84929 / 2.65 ( 156) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 610 Ramachandran restraints generated. 305 Oldfield, 0 Emsley, 305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 610 Ramachandran restraints generated. 305 Oldfield, 0 Emsley, 305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 35 time to evaluate : 0.075 Fit side-chains REVERT: A 6 GLN cc_start: 0.8274 (OUTLIER) cc_final: 0.7520 (mp10) REVERT: B 6 GLN cc_start: 0.8100 (OUTLIER) cc_final: 0.7607 (mp10) REVERT: C 9 ASN cc_start: 0.8670 (t0) cc_final: 0.8338 (t0) REVERT: E 6 GLN cc_start: 0.8317 (OUTLIER) cc_final: 0.7954 (mp10) outliers start: 6 outliers final: 0 residues processed: 38 average time/residue: 0.2373 time to fit residues: 9.3668 Evaluate side-chains 31 residues out of total 245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 28 time to evaluate : 0.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 GLN Chi-restraints excluded: chain B residue 6 GLN Chi-restraints excluded: chain E residue 6 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 29 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 20 optimal weight: 5.9990 chunk 18 optimal weight: 8.9990 chunk 15 optimal weight: 5.9990 chunk 16 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 21 ASN A 27 ASN ** A 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 11 GLN ** B 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 21 ASN C 9 ASN C 11 GLN ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 21 ASN ** D 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 9 ASN D 11 GLN ** D 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 21 ASN D 23 GLN ** E 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 9 ASN E 11 GLN E 27 ASN E 47 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.105312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.083500 restraints weight = 3472.550| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 2.10 r_work: 0.3297 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3188 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.1668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.027 2640 Z= 0.324 Angle : 0.497 5.020 3565 Z= 0.285 Chirality : 0.036 0.079 265 Planarity : 0.003 0.022 540 Dihedral : 7.264 54.858 394 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 4.90 % Allowed : 14.69 % Favored : 80.41 % 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 are not related in a simple way. whole: -3.68 (0.25), residues: 305 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.80 (0.19), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG E 28 TYR 0.022 0.002 TYR E 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00696 / 0.32 ( 2640) covalent geometry : angle 0.49690 / 0.29 ( 3565) hydrogen bonds : bond 0.02794 / 1.84 ( 52) hydrogen bonds : angle 4.00228 / 2.73 ( 156) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 610 Ramachandran restraints generated. 305 Oldfield, 0 Emsley, 305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 610 Ramachandran restraints generated. 305 Oldfield, 0 Emsley, 305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 29 time to evaluate : 0.095 Fit side-chains REVERT: A 6 GLN cc_start: 0.8232 (OUTLIER) cc_final: 0.7339 (mp10) REVERT: A 30 GLN cc_start: 0.8828 (mt0) cc_final: 0.8576 (mt0) REVERT: B 6 GLN cc_start: 0.8161 (OUTLIER) cc_final: 0.7779 (mp10) REVERT: C 47 GLN cc_start: 0.8949 (OUTLIER) cc_final: 0.8650 (tt0) REVERT: D 6 GLN cc_start: 0.8026 (mp10) cc_final: 0.7100 (mp10) REVERT: D 21 ASN cc_start: 0.9074 (OUTLIER) cc_final: 0.8873 (m110) REVERT: E 6 GLN cc_start: 0.8292 (OUTLIER) cc_final: 0.7862 (mp10) REVERT: E 21 ASN cc_start: 0.9348 (OUTLIER) cc_final: 0.9082 (m-40) REVERT: E 23 GLN cc_start: 0.9189 (tt0) cc_final: 0.8917 (tt0) outliers start: 12 outliers final: 0 residues processed: 39 average time/residue: 0.5166 time to fit residues: 20.7025 Evaluate side-chains 31 residues out of total 245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 25 time to evaluate : 0.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 GLN Chi-restraints excluded: chain B residue 6 GLN Chi-restraints excluded: chain C residue 47 GLN Chi-restraints excluded: chain D residue 21 ASN Chi-restraints excluded: chain E residue 6 GLN Chi-restraints excluded: chain E residue 21 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 27 optimal weight: 3.9990 chunk 1 optimal weight: 0.6980 chunk 12 optimal weight: 5.9990 chunk 26 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 5 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 11 GLN A 27 ASN ** B 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 21 ASN B 23 GLN ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 21 ASN ** D 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 21 ASN D 23 GLN ** E 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.106399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.084600 restraints weight = 3375.782| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 2.09 r_work: 0.3313 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3205 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.1779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.021 2640 Z= 0.260 Angle : 0.470 4.640 3565 Z= 0.269 Chirality : 0.035 0.076 265 Planarity : 0.003 0.028 540 Dihedral : 7.264 58.360 394 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 5.31 % Allowed : 13.88 % Favored : 80.82 % 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 are not related in a simple way. whole: -3.62 (0.26), residues: 305 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.75 (0.20), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.002 ARG A 28 TYR 0.020 0.002 TYR E 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00558 / 0.26 ( 2640) covalent geometry : angle 0.46985 / 0.27 ( 3565) hydrogen bonds : bond 0.02512 / 1.66 ( 52) hydrogen bonds : angle 3.97398 / 2.73 ( 156) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 610 Ramachandran restraints generated. 305 Oldfield, 0 Emsley, 305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 610 Ramachandran restraints generated. 305 Oldfield, 0 Emsley, 305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 28 time to evaluate : 0.095 Fit side-chains REVERT: A 6 GLN cc_start: 0.8212 (OUTLIER) cc_final: 0.7473 (mp10) REVERT: B 6 GLN cc_start: 0.8185 (OUTLIER) cc_final: 0.7706 (mp10) REVERT: C 47 GLN cc_start: 0.8937 (OUTLIER) cc_final: 0.8637 (tt0) REVERT: C 53 SER cc_start: 0.9340 (m) cc_final: 0.9104 (m) REVERT: D 6 GLN cc_start: 0.8018 (mp10) cc_final: 0.7741 (mp10) REVERT: D 21 ASN cc_start: 0.9005 (OUTLIER) cc_final: 0.8782 (m110) REVERT: E 6 GLN cc_start: 0.8372 (OUTLIER) cc_final: 0.8039 (mp10) REVERT: E 21 ASN cc_start: 0.9331 (OUTLIER) cc_final: 0.9023 (m-40) REVERT: E 23 GLN cc_start: 0.8989 (tt0) cc_final: 0.8565 (tt0) outliers start: 13 outliers final: 1 residues processed: 39 average time/residue: 0.4918 time to fit residues: 19.7863 Evaluate side-chains 35 residues out of total 245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 28 time to evaluate : 0.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 GLN Chi-restraints excluded: chain B residue 6 GLN Chi-restraints excluded: chain C residue 47 GLN Chi-restraints excluded: chain D residue 21 ASN Chi-restraints excluded: chain E residue 6 GLN Chi-restraints excluded: chain E residue 19 ASN Chi-restraints excluded: chain E residue 21 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 21 optimal weight: 3.9990 chunk 6 optimal weight: 10.0000 chunk 0 optimal weight: 0.6980 chunk 18 optimal weight: 10.0000 chunk 14 optimal weight: 0.5980 chunk 12 optimal weight: 0.9980 chunk 13 optimal weight: 0.7980 chunk 15 optimal weight: 0.8980 chunk 8 optimal weight: 0.6980 chunk 22 optimal weight: 0.9980 chunk 2 optimal weight: 4.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 21 ASN A 27 ASN ** B 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 21 ASN ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 19 ASN C 21 ASN ** D 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 21 ASN D 23 GLN D 30 GLN ** E 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.109157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.087475 restraints weight = 3319.639| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 2.09 r_work: 0.3369 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3263 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.1862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 2640 Z= 0.128 Angle : 0.429 4.444 3565 Z= 0.243 Chirality : 0.034 0.077 265 Planarity : 0.003 0.042 540 Dihedral : 7.062 59.327 394 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 5.31 % Allowed : 13.88 % Favored : 80.82 % 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 are not related in a simple way. whole: -3.56 (0.27), residues: 305 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.70 (0.21), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.002 ARG A 28 TYR 0.023 0.001 TYR E 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.13 ( 2640) covalent geometry : angle 0.42876 / 0.24 ( 3565) hydrogen bonds : bond 0.02126 / 1.40 ( 52) hydrogen bonds : angle 3.79282 / 2.62 ( 156) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 610 Ramachandran restraints generated. 305 Oldfield, 0 Emsley, 305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 610 Ramachandran restraints generated. 305 Oldfield, 0 Emsley, 305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 24 time to evaluate : 0.096 Fit side-chains REVERT: A 6 GLN cc_start: 0.8169 (OUTLIER) cc_final: 0.7521 (mp10) REVERT: A 28 ARG cc_start: 0.8529 (mtp-110) cc_final: 0.6802 (ttp-110) REVERT: B 6 GLN cc_start: 0.8215 (OUTLIER) cc_final: 0.7818 (mp10) REVERT: C 53 SER cc_start: 0.9303 (m) cc_final: 0.9091 (m) REVERT: D 6 GLN cc_start: 0.7934 (OUTLIER) cc_final: 0.7616 (mp10) REVERT: E 6 GLN cc_start: 0.8325 (OUTLIER) cc_final: 0.7915 (mp10) REVERT: E 23 GLN cc_start: 0.8859 (tt0) cc_final: 0.8590 (tt0) outliers start: 13 outliers final: 1 residues processed: 35 average time/residue: 0.4643 time to fit residues: 16.7385 Evaluate side-chains 32 residues out of total 245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 27 time to evaluate : 0.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 GLN Chi-restraints excluded: chain B residue 6 GLN Chi-restraints excluded: chain B residue 60 TYR Chi-restraints excluded: chain D residue 6 GLN Chi-restraints excluded: chain E residue 6 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 7 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 10 optimal weight: 0.2980 chunk 28 optimal weight: 0.9990 chunk 8 optimal weight: 0.7980 chunk 12 optimal weight: 6.9990 chunk 14 optimal weight: 0.9980 chunk 3 optimal weight: 2.9990 chunk 18 optimal weight: 0.0980 chunk 0 optimal weight: 8.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 21 ASN A 27 ASN ** B 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 19 ASN B 21 ASN ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 19 ASN C 21 ASN ** D 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 21 ASN D 23 GLN E 19 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.110367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.089271 restraints weight = 3337.993| |-----------------------------------------------------------------------------| r_work (start): 0.3533 rms_B_bonded: 2.06 r_work: 0.3417 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3310 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.1949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 2640 Z= 0.113 Angle : 0.414 4.641 3565 Z= 0.234 Chirality : 0.034 0.076 265 Planarity : 0.003 0.040 540 Dihedral : 6.971 61.000 394 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 4.49 % Allowed : 16.33 % Favored : 79.18 % 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 are not related in a simple way. whole: -3.51 (0.28), residues: 305 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.66 (0.22), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.002 ARG C 28 TYR 0.024 0.001 TYR E 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 ( 2640) covalent geometry : angle 0.41432 / 0.23 ( 3565) hydrogen bonds : bond 0.01927 / 1.27 ( 52) hydrogen bonds : angle 3.67748 / 2.55 ( 156) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 610 Ramachandran restraints generated. 305 Oldfield, 0 Emsley, 305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 610 Ramachandran restraints generated. 305 Oldfield, 0 Emsley, 305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 29 time to evaluate : 0.114 Fit side-chains REVERT: A 6 GLN cc_start: 0.8091 (OUTLIER) cc_final: 0.7572 (mp10) REVERT: B 6 GLN cc_start: 0.8223 (OUTLIER) cc_final: 0.7788 (mp10) REVERT: C 47 GLN cc_start: 0.8893 (OUTLIER) cc_final: 0.8595 (tt0) REVERT: D 6 GLN cc_start: 0.7995 (OUTLIER) cc_final: 0.7712 (mp10) REVERT: D 21 ASN cc_start: 0.8871 (OUTLIER) cc_final: 0.8603 (m110) REVERT: E 6 GLN cc_start: 0.8316 (OUTLIER) cc_final: 0.7952 (mp10) REVERT: E 21 ASN cc_start: 0.9257 (OUTLIER) cc_final: 0.8917 (m-40) outliers start: 11 outliers final: 1 residues processed: 37 average time/residue: 0.5528 time to fit residues: 20.9817 Evaluate side-chains 31 residues out of total 245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 23 time to evaluate : 0.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 GLN Chi-restraints excluded: chain B residue 6 GLN Chi-restraints excluded: chain B residue 60 TYR Chi-restraints excluded: chain C residue 47 GLN Chi-restraints excluded: chain D residue 6 GLN Chi-restraints excluded: chain D residue 21 ASN Chi-restraints excluded: chain E residue 6 GLN Chi-restraints excluded: chain E residue 21 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 18 optimal weight: 7.9990 chunk 8 optimal weight: 5.9990 chunk 22 optimal weight: 3.9990 chunk 6 optimal weight: 10.0000 chunk 23 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 10 optimal weight: 0.7980 chunk 9 optimal weight: 0.7980 chunk 2 optimal weight: 0.8980 chunk 13 optimal weight: 0.7980 chunk 27 optimal weight: 4.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 21 ASN A 27 ASN ** B 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 19 ASN ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 19 ASN ** D 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 21 ASN D 23 GLN D 30 GLN D 56 GLN ** E 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 19 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.108059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.086464 restraints weight = 3363.580| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 2.09 r_work: 0.3366 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3259 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.2008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.019 2640 Z= 0.193 Angle : 0.438 4.509 3565 Z= 0.249 Chirality : 0.035 0.076 265 Planarity : 0.003 0.039 540 Dihedral : 7.081 62.737 394 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 5.31 % Allowed : 16.33 % Favored : 78.37 % 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 are not related in a simple way. whole: -3.51 (0.28), residues: 305 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.67 (0.22), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.002 ARG C 28 TYR 0.026 0.001 TYR E 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.19 ( 2640) covalent geometry : angle 0.43757 / 0.25 ( 3565) hydrogen bonds : bond 0.02053 / 1.36 ( 52) hydrogen bonds : angle 3.75401 / 2.61 ( 156) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 610 Ramachandran restraints generated. 305 Oldfield, 0 Emsley, 305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 610 Ramachandran restraints generated. 305 Oldfield, 0 Emsley, 305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 24 time to evaluate : 0.096 Fit side-chains REVERT: B 6 GLN cc_start: 0.8278 (OUTLIER) cc_final: 0.7882 (mp10) REVERT: C 47 GLN cc_start: 0.8917 (OUTLIER) cc_final: 0.8616 (tt0) REVERT: C 53 SER cc_start: 0.9300 (m) cc_final: 0.9083 (m) REVERT: D 6 GLN cc_start: 0.7949 (OUTLIER) cc_final: 0.7659 (mp10) REVERT: E 6 GLN cc_start: 0.8310 (OUTLIER) cc_final: 0.7955 (mp10) outliers start: 13 outliers final: 1 residues processed: 35 average time/residue: 0.5570 time to fit residues: 20.0029 Evaluate side-chains 30 residues out of total 245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 25 time to evaluate : 0.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 6 GLN Chi-restraints excluded: chain B residue 60 TYR Chi-restraints excluded: chain C residue 47 GLN Chi-restraints excluded: chain D residue 6 GLN Chi-restraints excluded: chain E residue 6 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 29 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 17 optimal weight: 0.6980 chunk 12 optimal weight: 10.0000 chunk 2 optimal weight: 4.9990 chunk 15 optimal weight: 4.9990 chunk 28 optimal weight: 0.7980 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 21 ASN ** B 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 19 ASN B 30 GLN ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 19 ASN ** D 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 30 GLN ** E 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 19 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.104752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.084188 restraints weight = 3512.013| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 2.00 r_work: 0.3334 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3227 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.2106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.029 2640 Z= 0.255 Angle : 0.480 5.126 3565 Z= 0.271 Chirality : 0.035 0.076 265 Planarity : 0.003 0.037 540 Dihedral : 6.292 58.502 391 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 3.67 % Allowed : 17.96 % Favored : 78.37 % 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 are not related in a simple way. whole: -3.54 (0.28), residues: 305 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.69 (0.22), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.003 ARG B 28 TYR 0.026 0.002 TYR E 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00552 / 0.25 ( 2640) covalent geometry : angle 0.47956 / 0.27 ( 3565) hydrogen bonds : bond 0.02283 / 1.51 ( 52) hydrogen bonds : angle 3.88093 / 2.70 ( 156) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 610 Ramachandran restraints generated. 305 Oldfield, 0 Emsley, 305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 610 Ramachandran restraints generated. 305 Oldfield, 0 Emsley, 305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 26 time to evaluate : 0.094 Fit side-chains REVERT: B 6 GLN cc_start: 0.8289 (OUTLIER) cc_final: 0.7930 (mp10) REVERT: B 28 ARG cc_start: 0.7977 (mtp-110) cc_final: 0.7212 (tpt-90) REVERT: C 47 GLN cc_start: 0.8920 (OUTLIER) cc_final: 0.8622 (tt0) REVERT: C 53 SER cc_start: 0.9323 (m) cc_final: 0.9072 (m) REVERT: D 6 GLN cc_start: 0.8015 (OUTLIER) cc_final: 0.7739 (mp10) REVERT: E 6 GLN cc_start: 0.8407 (OUTLIER) cc_final: 0.8174 (mp10) REVERT: E 23 GLN cc_start: 0.8990 (tt0) cc_final: 0.8506 (tt0) outliers start: 9 outliers final: 1 residues processed: 32 average time/residue: 0.4263 time to fit residues: 14.0582 Evaluate side-chains 32 residues out of total 245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 27 time to evaluate : 0.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 6 GLN Chi-restraints excluded: chain B residue 60 TYR Chi-restraints excluded: chain C residue 47 GLN Chi-restraints excluded: chain D residue 6 GLN Chi-restraints excluded: chain E residue 6 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 12 optimal weight: 9.9990 chunk 24 optimal weight: 10.0000 chunk 19 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 chunk 0 optimal weight: 6.9990 chunk 23 optimal weight: 0.9980 chunk 4 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 20 optimal weight: 0.7980 chunk 14 optimal weight: 0.9990 chunk 11 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 21 ASN ** B 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 19 ASN C 8 ASN ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 19 ASN ** D 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 30 GLN ** E 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 19 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.109153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.087468 restraints weight = 3431.077| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 2.10 r_work: 0.3383 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3274 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.2104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2640 Z= 0.143 Angle : 0.440 4.444 3565 Z= 0.248 Chirality : 0.034 0.076 265 Planarity : 0.003 0.044 540 Dihedral : 6.114 60.800 391 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 4.08 % Allowed : 17.96 % Favored : 77.96 % 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 are not related in a simple way. whole: -3.54 (0.28), residues: 305 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.69 (0.22), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.003 ARG B 28 TYR 0.028 0.001 TYR C 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 ( 2640) covalent geometry : angle 0.43978 / 0.25 ( 3565) hydrogen bonds : bond 0.01983 / 1.31 ( 52) hydrogen bonds : angle 3.72753 / 2.59 ( 156) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 610 Ramachandran restraints generated. 305 Oldfield, 0 Emsley, 305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 610 Ramachandran restraints generated. 305 Oldfield, 0 Emsley, 305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 28 time to evaluate : 0.100 Fit side-chains REVERT: A 6 GLN cc_start: 0.8163 (mp10) cc_final: 0.7618 (mp10) REVERT: B 6 GLN cc_start: 0.8254 (OUTLIER) cc_final: 0.7842 (mp10) REVERT: B 28 ARG cc_start: 0.7943 (mtp-110) cc_final: 0.6894 (ttm170) REVERT: C 47 GLN cc_start: 0.8904 (OUTLIER) cc_final: 0.8597 (tt0) REVERT: C 53 SER cc_start: 0.9266 (m) cc_final: 0.9045 (m) REVERT: D 6 GLN cc_start: 0.7971 (OUTLIER) cc_final: 0.7699 (mp10) REVERT: E 6 GLN cc_start: 0.8299 (OUTLIER) cc_final: 0.7943 (mp10) REVERT: E 21 ASN cc_start: 0.9251 (OUTLIER) cc_final: 0.8911 (m-40) outliers start: 10 outliers final: 1 residues processed: 35 average time/residue: 0.5968 time to fit residues: 21.4198 Evaluate side-chains 32 residues out of total 245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 26 time to evaluate : 0.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 6 GLN Chi-restraints excluded: chain B residue 60 TYR Chi-restraints excluded: chain C residue 47 GLN Chi-restraints excluded: chain D residue 6 GLN Chi-restraints excluded: chain E residue 6 GLN Chi-restraints excluded: chain E residue 21 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 17 optimal weight: 3.9990 chunk 23 optimal weight: 0.6980 chunk 29 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 13 optimal weight: 0.8980 chunk 12 optimal weight: 4.9990 chunk 5 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 3 optimal weight: 0.8980 chunk 2 optimal weight: 3.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 21 ASN A 27 ASN ** B 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 19 ASN B 30 GLN C 8 ASN ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 19 ASN ** D 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 30 GLN ** E 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 19 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.108977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.087630 restraints weight = 3414.373| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 2.05 r_work: 0.3384 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3275 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.2150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2640 Z= 0.145 Angle : 0.445 4.560 3565 Z= 0.250 Chirality : 0.034 0.076 265 Planarity : 0.003 0.045 540 Dihedral : 6.103 61.714 391 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 4.08 % Allowed : 17.96 % Favored : 77.96 % 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 are not related in a simple way. whole: -3.53 (0.29), residues: 305 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.68 (0.22), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.003 ARG B 28 TYR 0.030 0.001 TYR C 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.15 ( 2640) covalent geometry : angle 0.44483 / 0.25 ( 3565) hydrogen bonds : bond 0.01993 / 1.31 ( 52) hydrogen bonds : angle 3.71241 / 2.60 ( 156) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 610 Ramachandran restraints generated. 305 Oldfield, 0 Emsley, 305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 610 Ramachandran restraints generated. 305 Oldfield, 0 Emsley, 305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 27 time to evaluate : 0.057 Fit side-chains REVERT: A 6 GLN cc_start: 0.8223 (mp10) cc_final: 0.7874 (mp10) REVERT: B 6 GLN cc_start: 0.8266 (OUTLIER) cc_final: 0.7860 (mp10) REVERT: B 28 ARG cc_start: 0.7838 (mtp-110) cc_final: 0.7148 (tpt-90) REVERT: C 47 GLN cc_start: 0.8896 (OUTLIER) cc_final: 0.8585 (tt0) REVERT: C 53 SER cc_start: 0.9270 (m) cc_final: 0.9052 (m) REVERT: D 6 GLN cc_start: 0.7963 (OUTLIER) cc_final: 0.7695 (mp10) REVERT: E 6 GLN cc_start: 0.8247 (OUTLIER) cc_final: 0.7904 (mp10) REVERT: E 21 ASN cc_start: 0.9231 (OUTLIER) cc_final: 0.8884 (m-40) outliers start: 10 outliers final: 1 residues processed: 34 average time/residue: 0.5818 time to fit residues: 20.2763 Evaluate side-chains 32 residues out of total 245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 26 time to evaluate : 0.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 6 GLN Chi-restraints excluded: chain B residue 60 TYR Chi-restraints excluded: chain C residue 47 GLN Chi-restraints excluded: chain D residue 6 GLN Chi-restraints excluded: chain E residue 6 GLN Chi-restraints excluded: chain E residue 21 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 2 optimal weight: 3.9990 chunk 22 optimal weight: 0.5980 chunk 7 optimal weight: 0.9990 chunk 27 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 18 optimal weight: 4.9990 chunk 10 optimal weight: 0.5980 chunk 23 optimal weight: 4.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 21 ASN ** B 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 19 ASN C 8 ASN ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 19 ASN ** D 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 30 GLN ** E 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 19 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.108776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.086956 restraints weight = 3377.503| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 2.09 r_work: 0.3365 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3259 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.2133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 2640 Z= 0.165 Angle : 0.447 4.610 3565 Z= 0.252 Chirality : 0.034 0.076 265 Planarity : 0.003 0.043 540 Dihedral : 6.146 63.233 391 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 4.08 % Allowed : 17.96 % Favored : 77.96 % 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 are not related in a simple way. whole: -3.52 (0.28), residues: 305 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.68 (0.22), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.003 ARG B 28 TYR 0.030 0.001 TYR C 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.17 ( 2640) covalent geometry : angle 0.44743 / 0.25 ( 3565) hydrogen bonds : bond 0.02025 / 1.33 ( 52) hydrogen bonds : angle 3.72491 / 2.60 ( 156) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1088.46 seconds wall clock time: 19 minutes 25.51 seconds (1165.51 seconds total)