Starting phenix.real_space_refine on Sun Apr 5 00:39:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9rba_53889/04_2026/9rba_53889.cif Found real_map, /net/cci-nas-00/data/ceres_data/9rba_53889/04_2026/9rba_53889.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9rba_53889/04_2026/9rba_53889.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9rba_53889/04_2026/9rba_53889.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9rba_53889/04_2026/9rba_53889.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9rba_53889/04_2026/9rba_53889.map" } resolution = 3.54 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= 0.000 sd= 0.004 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 C 1940 2.51 5 N 540 2.21 5 O 610 1.98 5 H 3300 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6390 Number of models: 1 Model: "" Number of chains: 1 Chain: "C" Number of atoms: 639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 639 Classifications: {'peptide': 44} Link IDs: {'TRANS': 43} Restraints were copied for chains: A, B, D, E, F, G, H, I, J Time building chain proxies: 0.50, per 1000 atoms: 0.08 Number of scatterers: 6390 At special positions: 0 Unit cell: (57.368, 97.768, 40.4, 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) O 610 8.00 N 540 7.00 C 1940 6.00 H 3300 1.00 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: 0.50 Conformation dependent library (CDL) restraints added in 238.1 milliseconds 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 760 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 12 sheets defined 0.0% alpha, 31.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 38 through 39 removed outlier: 7.069A pdb=" N LEU A 38 " --> pdb=" O TYR B 39 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N LEU C 38 " --> pdb=" O TYR D 39 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N LEU D 38 " --> pdb=" O TYR E 39 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 50 removed outlier: 6.615A pdb=" N VAL C 48 " --> pdb=" O VAL B 49 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 55 removed outlier: 6.237A pdb=" N THR A 54 " --> pdb=" O VAL B 55 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N THR C 54 " --> pdb=" O VAL D 55 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N THR D 54 " --> pdb=" O VAL E 55 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 61 through 65 removed outlier: 6.337A pdb=" N GLN D 62 " --> pdb=" O VAL E 63 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N ASN E 65 " --> pdb=" O GLN D 62 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N THR D 64 " --> pdb=" O ASN E 65 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 71 through 72 removed outlier: 6.510A pdb=" N VAL C 71 " --> pdb=" O THR B 72 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 75 through 79 removed outlier: 6.233A pdb=" N THR A 75 " --> pdb=" O ALA B 76 " (cutoff:3.500A) removed outlier: 8.024A pdb=" N ALA B 78 " --> pdb=" O THR A 75 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N VAL A 77 " --> pdb=" O ALA B 78 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N THR C 75 " --> pdb=" O ALA D 76 " (cutoff:3.500A) removed outlier: 8.095A pdb=" N ALA D 78 " --> pdb=" O THR C 75 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N VAL C 77 " --> pdb=" O ALA D 78 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N THR D 75 " --> pdb=" O ALA E 76 " (cutoff:3.500A) removed outlier: 8.059A pdb=" N ALA E 78 " --> pdb=" O THR D 75 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N VAL D 77 " --> pdb=" O ALA E 78 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 38 through 39 removed outlier: 6.916A pdb=" N LEU F 38 " --> pdb=" O TYR G 39 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N LEU G 38 " --> pdb=" O TYR H 39 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N LEU H 38 " --> pdb=" O TYR I 39 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N LEU I 38 " --> pdb=" O TYR J 39 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'F' and resid 48 through 50 removed outlier: 6.687A pdb=" N VAL G 49 " --> pdb=" O HIS H 50 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 53 through 55 removed outlier: 6.254A pdb=" N THR F 54 " --> pdb=" O VAL G 55 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N THR H 54 " --> pdb=" O VAL I 55 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N THR I 54 " --> pdb=" O VAL J 55 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 61 through 65 removed outlier: 6.421A pdb=" N GLN H 62 " --> pdb=" O VAL I 63 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N ASN I 65 " --> pdb=" O GLN H 62 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N THR H 64 " --> pdb=" O ASN I 65 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N GLN I 62 " --> pdb=" O VAL J 63 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N ASN J 65 " --> pdb=" O GLN I 62 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N THR I 64 " --> pdb=" O ASN J 65 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 71 through 72 Processing sheet with id=AB3, first strand: chain 'F' and resid 75 through 79 removed outlier: 6.268A pdb=" N THR F 75 " --> pdb=" O ALA G 76 " (cutoff:3.500A) removed outlier: 8.070A pdb=" N ALA G 78 " --> pdb=" O THR F 75 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N VAL F 77 " --> pdb=" O ALA G 78 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N THR G 75 " --> pdb=" O ALA H 76 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N ALA H 78 " --> pdb=" O THR G 75 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N VAL G 77 " --> pdb=" O ALA H 78 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N THR H 75 " --> pdb=" O ALA I 76 " (cutoff:3.500A) removed outlier: 8.258A pdb=" N ALA I 78 " --> pdb=" O THR H 75 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N VAL H 77 " --> pdb=" O ALA I 78 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N THR I 75 " --> pdb=" O ALA J 76 " (cutoff:3.500A) removed outlier: 8.066A pdb=" N ALA J 78 " --> pdb=" O THR I 75 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N VAL I 77 " --> pdb=" O ALA J 78 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 48 hydrogen bonds defined for protein. 144 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.22 Time building geometry restraints manager: 0.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.96 - 1.09: 800 1.09 - 1.21: 2810 1.21 - 1.34: 700 1.34 - 1.47: 421 1.47 - 1.60: 1669 Bond restraints: 6400 Sorted by residual: bond pdb=" N THR B 59 " pdb=" H THR B 59 " ideal model delta sigma weight residual 0.860 1.012 -0.152 2.00e-02 2.50e+03 5.74e+01 bond pdb=" N THR A 59 " pdb=" H THR A 59 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.73e+01 bond pdb=" N VAL B 74 " pdb=" H VAL B 74 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.73e+01 bond pdb=" CD2 TYR E 39 " pdb=" HD2 TYR E 39 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.73e+01 bond pdb=" N ALA H 53 " pdb=" H ALA H 53 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.73e+01 ... (remaining 6395 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.25: 9988 3.25 - 6.49: 1510 6.49 - 9.74: 122 9.74 - 12.98: 20 12.98 - 16.23: 20 Bond angle restraints: 11660 Sorted by residual: angle pdb=" N GLY G 68 " pdb=" CA GLY G 68 " pdb=" C GLY G 68 " ideal model delta sigma weight residual 112.48 128.71 -16.23 1.21e+00 6.83e-01 1.80e+02 angle pdb=" N GLY C 68 " pdb=" CA GLY C 68 " pdb=" C GLY C 68 " ideal model delta sigma weight residual 112.48 128.71 -16.23 1.21e+00 6.83e-01 1.80e+02 angle pdb=" N GLY H 68 " pdb=" CA GLY H 68 " pdb=" C GLY H 68 " ideal model delta sigma weight residual 112.48 128.70 -16.22 1.21e+00 6.83e-01 1.80e+02 angle pdb=" N GLY I 68 " pdb=" CA GLY I 68 " pdb=" C GLY I 68 " ideal model delta sigma weight residual 112.48 128.69 -16.21 1.21e+00 6.83e-01 1.79e+02 angle pdb=" N GLY D 68 " pdb=" CA GLY D 68 " pdb=" C GLY D 68 " ideal model delta sigma weight residual 112.48 128.69 -16.21 1.21e+00 6.83e-01 1.79e+02 ... (remaining 11655 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.39: 2440 15.39 - 30.78: 220 30.78 - 46.17: 60 46.17 - 61.56: 180 61.56 - 76.95: 20 Dihedral angle restraints: 2920 sinusoidal: 1650 harmonic: 1270 Sorted by residual: dihedral pdb=" C VAL E 52 " pdb=" N VAL E 52 " pdb=" CA VAL E 52 " pdb=" CB VAL E 52 " ideal model delta harmonic sigma weight residual -122.00 -112.31 -9.69 0 2.50e+00 1.60e-01 1.50e+01 dihedral pdb=" C VAL F 52 " pdb=" N VAL F 52 " pdb=" CA VAL F 52 " pdb=" CB VAL F 52 " ideal model delta harmonic sigma weight residual -122.00 -112.32 -9.68 0 2.50e+00 1.60e-01 1.50e+01 dihedral pdb=" C VAL I 52 " pdb=" N VAL I 52 " pdb=" CA VAL I 52 " pdb=" CB VAL I 52 " ideal model delta harmonic sigma weight residual -122.00 -112.34 -9.66 0 2.50e+00 1.60e-01 1.49e+01 ... (remaining 2917 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.107: 410 0.107 - 0.214: 120 0.214 - 0.320: 20 0.320 - 0.427: 10 0.427 - 0.534: 10 Chirality restraints: 570 Sorted by residual: chirality pdb=" CA ALA A 69 " pdb=" N ALA A 69 " pdb=" C ALA A 69 " pdb=" CB ALA A 69 " both_signs ideal model delta sigma weight residual False 2.48 1.95 0.53 2.00e-01 2.50e+01 7.13e+00 chirality pdb=" CA ALA I 69 " pdb=" N ALA I 69 " pdb=" C ALA I 69 " pdb=" CB ALA I 69 " both_signs ideal model delta sigma weight residual False 2.48 1.95 0.53 2.00e-01 2.50e+01 7.10e+00 chirality pdb=" CA ALA H 69 " pdb=" N ALA H 69 " pdb=" C ALA H 69 " pdb=" CB ALA H 69 " both_signs ideal model delta sigma weight residual False 2.48 1.95 0.53 2.00e-01 2.50e+01 7.07e+00 ... (remaining 567 not shown) Planarity restraints: 940 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR G 59 " -0.013 2.00e-02 2.50e+03 2.63e-02 6.93e+00 pdb=" C THR G 59 " 0.046 2.00e-02 2.50e+03 pdb=" O THR G 59 " -0.017 2.00e-02 2.50e+03 pdb=" N LYS G 60 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 59 " 0.013 2.00e-02 2.50e+03 2.63e-02 6.90e+00 pdb=" C THR B 59 " -0.045 2.00e-02 2.50e+03 pdb=" O THR B 59 " 0.017 2.00e-02 2.50e+03 pdb=" N LYS B 60 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR H 59 " -0.013 2.00e-02 2.50e+03 2.62e-02 6.86e+00 pdb=" C THR H 59 " 0.045 2.00e-02 2.50e+03 pdb=" O THR H 59 " -0.017 2.00e-02 2.50e+03 pdb=" N LYS H 60 " -0.015 2.00e-02 2.50e+03 ... (remaining 937 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.15: 346 2.15 - 2.74: 10329 2.74 - 3.33: 17390 3.33 - 3.91: 22960 3.91 - 4.50: 31364 Nonbonded interactions: 82389 Sorted by model distance: nonbonded pdb=" HA THR C 75 " pdb="HG21 THR B 75 " model vdw 1.567 2.440 nonbonded pdb="HG21 THR H 75 " pdb=" HA THR I 75 " model vdw 1.572 2.440 nonbonded pdb="HG21 THR I 75 " pdb=" HA THR J 75 " model vdw 1.591 2.440 nonbonded pdb="HG21 THR D 75 " pdb=" HA THR E 75 " model vdw 1.610 2.440 nonbonded pdb="HG21 THR F 75 " pdb=" HA THR G 75 " model vdw 1.616 2.440 ... (remaining 82384 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: 0.01 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'A' selection = chain 'B' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 6.850 Find NCS groups from input model: 0.030 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:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6620 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 : 0.023 0.129 3100 Z= 1.412 Angle : 2.746 16.230 4200 Z= 1.992 Chirality : 0.128 0.534 570 Planarity : 0.010 0.026 510 Dihedral : 10.296 39.700 1060 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 3.03 % Allowed : 6.06 % Favored : 90.91 % 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: -2.74 (0.25), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.08 (0.19), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.006 0.003 TYR I 39 HIS 0.003 0.002 HIS F 50 Details of bonding type rmsd covalent geometry : bond 0.02260 ( 3100) covalent geometry : angle 2.74636 ( 4200) hydrogen bonds : bond 0.15087 ( 48) hydrogen bonds : angle 5.29250 ( 144) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 143 time to evaluate : 0.178 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 43 LYS cc_start: 0.7167 (tttt) cc_final: 0.6954 (ttmt) REVERT: C 79 GLN cc_start: 0.7365 (tt0) cc_final: 0.6543 (mt0) REVERT: A 57 GLU cc_start: 0.7611 (mt-10) cc_final: 0.7321 (mp0) REVERT: A 79 GLN cc_start: 0.7686 (tt0) cc_final: 0.6972 (mt0) REVERT: A 80 LYS cc_start: 0.7681 (mttp) cc_final: 0.7358 (tttt) REVERT: B 45 LYS cc_start: 0.6753 (tttm) cc_final: 0.6531 (tmtt) REVERT: B 79 GLN cc_start: 0.7554 (tt0) cc_final: 0.6893 (mt0) REVERT: D 79 GLN cc_start: 0.7433 (tt0) cc_final: 0.6664 (mt0) REVERT: E 79 GLN cc_start: 0.8167 (tt0) cc_final: 0.7730 (mt0) REVERT: F 57 GLU cc_start: 0.7642 (mt-10) cc_final: 0.7251 (mp0) REVERT: F 79 GLN cc_start: 0.7637 (tt0) cc_final: 0.6956 (mt0) REVERT: F 80 LYS cc_start: 0.7926 (mttp) cc_final: 0.7505 (tttt) REVERT: G 79 GLN cc_start: 0.7543 (tt0) cc_final: 0.6852 (mt0) REVERT: H 79 GLN cc_start: 0.7514 (tt0) cc_final: 0.7123 (tt0) REVERT: I 79 GLN cc_start: 0.7486 (tt0) cc_final: 0.6718 (mt0) REVERT: J 79 GLN cc_start: 0.8122 (tt0) cc_final: 0.7687 (mt0) outliers start: 10 outliers final: 0 residues processed: 153 average time/residue: 0.1734 time to fit residues: 31.0411 Evaluate side-chains 79 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 24 optimal weight: 5.9990 chunk 26 optimal weight: 5.9990 chunk 2 optimal weight: 5.9990 chunk 16 optimal weight: 6.9990 chunk 32 optimal weight: 5.9990 chunk 31 optimal weight: 3.9990 chunk 25 optimal weight: 5.9990 chunk 19 optimal weight: 4.9990 chunk 30 optimal weight: 5.9990 chunk 22 optimal weight: 5.9990 chunk 37 optimal weight: 5.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 65 ASN B 65 ASN D 65 ASN E 65 ASN G 65 ASN H 65 ASN I 65 ASN J 65 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.139905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.115962 restraints weight = 11463.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.122314 restraints weight = 4677.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.126984 restraints weight = 2506.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.130268 restraints weight = 1540.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.132625 restraints weight = 1019.210| |-----------------------------------------------------------------------------| r_work (final): 0.4546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.5476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 3100 Z= 0.266 Angle : 0.731 4.782 4200 Z= 0.447 Chirality : 0.057 0.131 570 Planarity : 0.003 0.010 510 Dihedral : 8.608 26.237 440 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 4.24 % Allowed : 13.64 % Favored : 82.12 % 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: -4.86 (0.23), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.70 (0.17), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.005 0.001 TYR B 39 HIS 0.002 0.001 HIS A 50 Details of bonding type rmsd covalent geometry : bond 0.00541 ( 3100) covalent geometry : angle 0.73086 ( 4200) hydrogen bonds : bond 0.03135 ( 48) hydrogen bonds : angle 4.19837 ( 144) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 67 time to evaluate : 0.182 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 10 residues processed: 70 average time/residue: 0.2080 time to fit residues: 16.8522 Evaluate side-chains 57 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 47 time to evaluate : 0.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain E residue 42 SER Chi-restraints excluded: chain F residue 42 SER Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain G residue 42 SER Chi-restraints excluded: chain H residue 42 SER Chi-restraints excluded: chain J residue 59 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 20 optimal weight: 9.9990 chunk 13 optimal weight: 10.0000 chunk 6 optimal weight: 5.9990 chunk 19 optimal weight: 4.9990 chunk 12 optimal weight: 10.0000 chunk 15 optimal weight: 0.8980 chunk 26 optimal weight: 8.9990 chunk 34 optimal weight: 5.9990 chunk 10 optimal weight: 3.9990 chunk 29 optimal weight: 7.9990 chunk 17 optimal weight: 5.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.131955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.107837 restraints weight = 11908.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.113961 restraints weight = 5136.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.118519 restraints weight = 2841.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.121833 restraints weight = 1780.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.124166 restraints weight = 1200.071| |-----------------------------------------------------------------------------| r_work (final): 0.4178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7118 moved from start: 0.7614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 3100 Z= 0.219 Angle : 0.671 5.080 4200 Z= 0.390 Chirality : 0.053 0.133 570 Planarity : 0.003 0.008 510 Dihedral : 7.972 23.873 440 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 3.64 % Allowed : 14.85 % Favored : 81.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.00 (0.27), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.81 (0.20), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.011 0.002 TYR F 39 HIS 0.001 0.000 HIS H 50 Details of bonding type rmsd covalent geometry : bond 0.00437 ( 3100) covalent geometry : angle 0.67121 ( 4200) hydrogen bonds : bond 0.02469 ( 48) hydrogen bonds : angle 3.95765 ( 144) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 45 time to evaluate : 0.178 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 LYS cc_start: 0.7835 (ttpp) cc_final: 0.7615 (ttpp) REVERT: A 79 GLN cc_start: 0.7662 (tt0) cc_final: 0.7319 (mt0) REVERT: B 79 GLN cc_start: 0.7876 (tt0) cc_final: 0.7229 (mp10) REVERT: G 79 GLN cc_start: 0.7748 (tt0) cc_final: 0.7316 (mt0) outliers start: 12 outliers final: 11 residues processed: 48 average time/residue: 0.0986 time to fit residues: 6.3785 Evaluate side-chains 51 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 40 time to evaluate : 0.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain E residue 42 SER Chi-restraints excluded: chain F residue 42 SER Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain G residue 42 SER Chi-restraints excluded: chain H residue 42 SER Chi-restraints excluded: chain J residue 42 SER Chi-restraints excluded: chain J residue 59 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 18 optimal weight: 7.9990 chunk 29 optimal weight: 9.9990 chunk 8 optimal weight: 10.0000 chunk 10 optimal weight: 10.0000 chunk 7 optimal weight: 5.9990 chunk 32 optimal weight: 9.9990 chunk 36 optimal weight: 2.9990 chunk 5 optimal weight: 6.9990 chunk 9 optimal weight: 6.9990 chunk 24 optimal weight: 9.9990 chunk 26 optimal weight: 6.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 65 ASN H 65 ASN I 65 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.131441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.107945 restraints weight = 11973.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.113936 restraints weight = 5197.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.118606 restraints weight = 2916.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.121823 restraints weight = 1808.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.124069 restraints weight = 1213.774| |-----------------------------------------------------------------------------| r_work (final): 0.4132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7295 moved from start: 0.8233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.035 3100 Z= 0.288 Angle : 0.731 4.815 4200 Z= 0.430 Chirality : 0.053 0.128 570 Planarity : 0.003 0.009 510 Dihedral : 8.505 27.481 440 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.62 % Favored : 87.38 % Rotamer: Outliers : 4.24 % Allowed : 15.45 % Favored : 80.30 % 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: -5.38 (0.27), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.09 (0.20), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.007 0.002 TYR G 39 HIS 0.003 0.001 HIS D 50 Details of bonding type rmsd covalent geometry : bond 0.00572 ( 3100) covalent geometry : angle 0.73074 ( 4200) hydrogen bonds : bond 0.03093 ( 48) hydrogen bonds : angle 4.36622 ( 144) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 38 time to evaluate : 0.185 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 GLN cc_start: 0.8106 (tt0) cc_final: 0.7686 (mt0) REVERT: G 79 GLN cc_start: 0.8142 (tt0) cc_final: 0.7773 (mt0) REVERT: H 79 GLN cc_start: 0.7839 (tt0) cc_final: 0.7120 (mp10) outliers start: 14 outliers final: 12 residues processed: 42 average time/residue: 0.0881 time to fit residues: 5.1502 Evaluate side-chains 47 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 35 time to evaluate : 0.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain D residue 42 SER Chi-restraints excluded: chain E residue 42 SER Chi-restraints excluded: chain F residue 42 SER Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain G residue 42 SER Chi-restraints excluded: chain H residue 42 SER Chi-restraints excluded: chain I residue 42 SER Chi-restraints excluded: chain J residue 42 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 17 optimal weight: 3.9990 chunk 18 optimal weight: 0.4980 chunk 32 optimal weight: 9.9990 chunk 2 optimal weight: 8.9990 chunk 29 optimal weight: 10.0000 chunk 11 optimal weight: 5.9990 chunk 23 optimal weight: 2.9990 chunk 5 optimal weight: 5.9990 chunk 12 optimal weight: 10.0000 chunk 38 optimal weight: 6.9990 chunk 10 optimal weight: 0.9980 overall best weight: 2.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4487 r_free = 0.4487 target = 0.147598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.122980 restraints weight = 11793.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.129452 restraints weight = 5390.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.134166 restraints weight = 3110.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4386 r_free = 0.4386 target = 0.137489 restraints weight = 2022.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4410 r_free = 0.4410 target = 0.139870 restraints weight = 1406.244| |-----------------------------------------------------------------------------| r_work (final): 0.4391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7459 moved from start: 0.8356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 3100 Z= 0.154 Angle : 0.613 4.157 4200 Z= 0.350 Chirality : 0.050 0.129 570 Planarity : 0.002 0.005 510 Dihedral : 7.499 23.214 440 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.95 % Favored : 89.05 % Rotamer: Outliers : 3.03 % Allowed : 16.97 % Favored : 80.00 % 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: -5.16 (0.27), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.93 (0.21), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.006 0.001 TYR H 39 HIS 0.001 0.001 HIS H 50 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 3100) covalent geometry : angle 0.61266 ( 4200) hydrogen bonds : bond 0.02144 ( 48) hydrogen bonds : angle 4.02978 ( 144) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 41 time to evaluate : 0.118 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 LYS cc_start: 0.7892 (mmtt) cc_final: 0.7221 (ttpp) REVERT: A 79 GLN cc_start: 0.8099 (tt0) cc_final: 0.7597 (mp10) REVERT: H 79 GLN cc_start: 0.7830 (tt0) cc_final: 0.7389 (mt0) outliers start: 10 outliers final: 9 residues processed: 42 average time/residue: 0.1071 time to fit residues: 6.0062 Evaluate side-chains 47 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 38 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain E residue 42 SER Chi-restraints excluded: chain F residue 42 SER Chi-restraints excluded: chain G residue 42 SER Chi-restraints excluded: chain H residue 42 SER Chi-restraints excluded: chain I residue 59 THR Chi-restraints excluded: chain J residue 42 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 24 optimal weight: 8.9990 chunk 13 optimal weight: 10.0000 chunk 35 optimal weight: 0.9980 chunk 18 optimal weight: 0.9980 chunk 14 optimal weight: 3.9990 chunk 21 optimal weight: 7.9990 chunk 7 optimal weight: 5.9990 chunk 19 optimal weight: 6.9990 chunk 12 optimal weight: 9.9990 chunk 33 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 overall best weight: 2.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4496 r_free = 0.4496 target = 0.148500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.124139 restraints weight = 11734.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.130577 restraints weight = 5509.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.135321 restraints weight = 3221.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4398 r_free = 0.4398 target = 0.138557 restraints weight = 2096.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.4423 r_free = 0.4423 target = 0.140971 restraints weight = 1464.139| |-----------------------------------------------------------------------------| r_work (final): 0.4417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.8524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 3100 Z= 0.161 Angle : 0.604 5.435 4200 Z= 0.344 Chirality : 0.050 0.129 570 Planarity : 0.002 0.006 510 Dihedral : 7.275 22.293 440 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.67 % Favored : 88.33 % Rotamer: Outliers : 2.42 % Allowed : 18.18 % Favored : 79.39 % 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: -5.07 (0.27), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.86 (0.21), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.007 0.001 TYR G 39 HIS 0.001 0.000 HIS D 50 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 3100) covalent geometry : angle 0.60419 ( 4200) hydrogen bonds : bond 0.02053 ( 48) hydrogen bonds : angle 3.90153 ( 144) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 36 time to evaluate : 0.178 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 60 LYS cc_start: 0.7958 (mmtt) cc_final: 0.7352 (ttpp) REVERT: A 79 GLN cc_start: 0.8126 (tt0) cc_final: 0.7667 (mp10) REVERT: G 79 GLN cc_start: 0.8119 (tt0) cc_final: 0.7686 (mp10) REVERT: H 58 LYS cc_start: 0.7957 (ttpp) cc_final: 0.7320 (mtpp) REVERT: H 79 GLN cc_start: 0.7906 (tt0) cc_final: 0.7500 (mt0) outliers start: 8 outliers final: 8 residues processed: 37 average time/residue: 0.1036 time to fit residues: 5.0312 Evaluate side-chains 42 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 34 time to evaluate : 0.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain E residue 42 SER Chi-restraints excluded: chain G residue 42 SER Chi-restraints excluded: chain H residue 42 SER Chi-restraints excluded: chain I residue 59 THR Chi-restraints excluded: chain J residue 42 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 19 optimal weight: 6.9990 chunk 39 optimal weight: 4.9990 chunk 7 optimal weight: 4.9990 chunk 33 optimal weight: 9.9990 chunk 29 optimal weight: 2.9990 chunk 20 optimal weight: 10.0000 chunk 13 optimal weight: 9.9990 chunk 3 optimal weight: 4.9990 chunk 15 optimal weight: 0.7980 chunk 23 optimal weight: 0.9990 chunk 32 optimal weight: 9.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4490 r_free = 0.4490 target = 0.148108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.123631 restraints weight = 11634.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.129839 restraints weight = 5602.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.134488 restraints weight = 3325.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4389 r_free = 0.4389 target = 0.137777 restraints weight = 2186.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4413 r_free = 0.4413 target = 0.140138 restraints weight = 1525.327| |-----------------------------------------------------------------------------| r_work (final): 0.4402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 moved from start: 0.8628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 3100 Z= 0.155 Angle : 0.596 5.399 4200 Z= 0.339 Chirality : 0.050 0.128 570 Planarity : 0.002 0.005 510 Dihedral : 7.109 21.700 440 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.90 % Favored : 88.10 % Rotamer: Outliers : 2.73 % Allowed : 17.88 % Favored : 79.39 % 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: -5.02 (0.27), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.82 (0.21), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.007 0.001 TYR C 39 HIS 0.001 0.000 HIS E 50 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 3100) covalent geometry : angle 0.59555 ( 4200) hydrogen bonds : bond 0.01952 ( 48) hydrogen bonds : angle 3.87920 ( 144) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 36 time to evaluate : 0.182 Fit side-chains revert: symmetry clash REVERT: A 60 LYS cc_start: 0.8004 (mmtt) cc_final: 0.7331 (ttpp) REVERT: A 79 GLN cc_start: 0.8153 (tt0) cc_final: 0.7703 (mt0) REVERT: G 79 GLN cc_start: 0.8244 (tt0) cc_final: 0.7728 (mt0) REVERT: H 58 LYS cc_start: 0.7915 (ttpp) cc_final: 0.7244 (mtpp) REVERT: H 79 GLN cc_start: 0.7958 (tt0) cc_final: 0.7534 (mt0) outliers start: 9 outliers final: 9 residues processed: 37 average time/residue: 0.1161 time to fit residues: 5.6775 Evaluate side-chains 44 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 35 time to evaluate : 0.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain E residue 42 SER Chi-restraints excluded: chain F residue 42 SER Chi-restraints excluded: chain G residue 42 SER Chi-restraints excluded: chain H residue 42 SER Chi-restraints excluded: chain I residue 59 THR Chi-restraints excluded: chain J residue 42 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 8 optimal weight: 6.9990 chunk 9 optimal weight: 9.9990 chunk 6 optimal weight: 4.9990 chunk 25 optimal weight: 10.0000 chunk 7 optimal weight: 0.6980 chunk 16 optimal weight: 9.9990 chunk 39 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 chunk 35 optimal weight: 5.9990 chunk 11 optimal weight: 0.9990 chunk 17 optimal weight: 8.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4496 r_free = 0.4496 target = 0.148967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.123835 restraints weight = 11650.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.130457 restraints weight = 5374.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4365 r_free = 0.4365 target = 0.135353 restraints weight = 3115.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4398 r_free = 0.4398 target = 0.138784 restraints weight = 2022.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4423 r_free = 0.4423 target = 0.141296 restraints weight = 1401.956| |-----------------------------------------------------------------------------| r_work (final): 0.4422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7484 moved from start: 0.8727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 3100 Z= 0.163 Angle : 0.599 5.326 4200 Z= 0.340 Chirality : 0.050 0.129 570 Planarity : 0.002 0.006 510 Dihedral : 7.047 21.494 440 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.90 % Favored : 88.10 % Rotamer: Outliers : 2.73 % Allowed : 17.27 % Favored : 80.00 % 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: -4.96 (0.27), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.77 (0.21), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.006 0.001 TYR C 39 HIS 0.001 0.000 HIS D 50 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 3100) covalent geometry : angle 0.59901 ( 4200) hydrogen bonds : bond 0.01992 ( 48) hydrogen bonds : angle 3.90464 ( 144) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 34 time to evaluate : 0.169 Fit side-chains revert: symmetry clash REVERT: A 60 LYS cc_start: 0.8006 (mmtt) cc_final: 0.7377 (ttpp) REVERT: A 79 GLN cc_start: 0.8252 (tt0) cc_final: 0.7783 (mt0) REVERT: G 79 GLN cc_start: 0.8299 (tt0) cc_final: 0.7641 (mt0) REVERT: H 58 LYS cc_start: 0.7928 (ttpp) cc_final: 0.7209 (mtpp) REVERT: H 79 GLN cc_start: 0.8031 (tt0) cc_final: 0.7623 (mt0) outliers start: 9 outliers final: 9 residues processed: 35 average time/residue: 0.1079 time to fit residues: 5.0449 Evaluate side-chains 43 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 34 time to evaluate : 0.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain E residue 42 SER Chi-restraints excluded: chain F residue 42 SER Chi-restraints excluded: chain G residue 42 SER Chi-restraints excluded: chain H residue 42 SER Chi-restraints excluded: chain I residue 59 THR Chi-restraints excluded: chain J residue 42 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 39 optimal weight: 6.9990 chunk 37 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 9 optimal weight: 10.0000 chunk 6 optimal weight: 0.7980 chunk 29 optimal weight: 10.0000 chunk 5 optimal weight: 5.9990 chunk 2 optimal weight: 6.9990 chunk 28 optimal weight: 10.0000 chunk 18 optimal weight: 6.9990 chunk 10 optimal weight: 0.9990 overall best weight: 4.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4422 r_free = 0.4422 target = 0.142416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.118230 restraints weight = 12341.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.124114 restraints weight = 6087.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.128503 restraints weight = 3653.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.131736 restraints weight = 2434.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.134064 restraints weight = 1715.861| |-----------------------------------------------------------------------------| r_work (final): 0.4380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.8850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 3100 Z= 0.215 Angle : 0.651 5.269 4200 Z= 0.369 Chirality : 0.051 0.128 570 Planarity : 0.002 0.008 510 Dihedral : 7.369 22.334 440 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.33 % Favored : 86.67 % Rotamer: Outliers : 2.73 % Allowed : 17.88 % Favored : 79.39 % 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: -5.12 (0.28), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.89 (0.21), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.006 0.001 TYR C 39 HIS 0.001 0.001 HIS D 50 Details of bonding type rmsd covalent geometry : bond 0.00422 ( 3100) covalent geometry : angle 0.65125 ( 4200) hydrogen bonds : bond 0.02393 ( 48) hydrogen bonds : angle 4.15751 ( 144) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 34 time to evaluate : 0.200 Fit side-chains REVERT: C 79 GLN cc_start: 0.7854 (tt0) cc_final: 0.7527 (mt0) REVERT: A 60 LYS cc_start: 0.8054 (mmtt) cc_final: 0.7474 (ttpp) REVERT: A 79 GLN cc_start: 0.8275 (tt0) cc_final: 0.7930 (mt0) REVERT: G 79 GLN cc_start: 0.8378 (tt0) cc_final: 0.7819 (mt0) REVERT: H 58 LYS cc_start: 0.8027 (ttpp) cc_final: 0.7251 (mtpp) REVERT: H 79 GLN cc_start: 0.8179 (tt0) cc_final: 0.7620 (mt0) outliers start: 9 outliers final: 9 residues processed: 35 average time/residue: 0.1107 time to fit residues: 5.1131 Evaluate side-chains 43 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 34 time to evaluate : 0.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain E residue 42 SER Chi-restraints excluded: chain F residue 42 SER Chi-restraints excluded: chain G residue 42 SER Chi-restraints excluded: chain H residue 42 SER Chi-restraints excluded: chain I residue 59 THR Chi-restraints excluded: chain J residue 42 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 10 optimal weight: 5.9990 chunk 15 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 34 optimal weight: 7.9990 chunk 13 optimal weight: 0.6980 chunk 23 optimal weight: 0.8980 chunk 20 optimal weight: 8.9990 chunk 32 optimal weight: 9.9990 chunk 2 optimal weight: 0.8980 chunk 25 optimal weight: 0.9980 chunk 7 optimal weight: 3.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 65 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4502 r_free = 0.4502 target = 0.147578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.122481 restraints weight = 11691.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.128680 restraints weight = 5714.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.133238 restraints weight = 3393.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.136656 restraints weight = 2258.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4419 r_free = 0.4419 target = 0.139132 restraints weight = 1589.222| |-----------------------------------------------------------------------------| r_work (final): 0.4443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7384 moved from start: 0.8815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 3100 Z= 0.097 Angle : 0.581 5.169 4200 Z= 0.318 Chirality : 0.051 0.131 570 Planarity : 0.001 0.004 510 Dihedral : 6.465 21.041 440 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.29 % Favored : 90.71 % Rotamer: Outliers : 0.91 % Allowed : 19.70 % Favored : 79.39 % 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: -4.60 (0.28), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.50 (0.22), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.007 0.001 TYR C 39 HIS 0.001 0.000 HIS E 50 Details of bonding type rmsd covalent geometry : bond 0.00202 ( 3100) covalent geometry : angle 0.58115 ( 4200) hydrogen bonds : bond 0.01420 ( 48) hydrogen bonds : angle 3.61801 ( 144) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 41 time to evaluate : 0.204 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 79 GLN cc_start: 0.7724 (tt0) cc_final: 0.7348 (mt0) REVERT: A 60 LYS cc_start: 0.7981 (mmtt) cc_final: 0.7389 (ttpp) REVERT: G 79 GLN cc_start: 0.8289 (tt0) cc_final: 0.7721 (mt0) REVERT: H 79 GLN cc_start: 0.8029 (tt0) cc_final: 0.7594 (mt0) outliers start: 3 outliers final: 2 residues processed: 41 average time/residue: 0.1009 time to fit residues: 5.5586 Evaluate side-chains 41 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 39 time to evaluate : 0.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain G residue 42 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 34 optimal weight: 7.9990 chunk 17 optimal weight: 7.9990 chunk 19 optimal weight: 0.6980 chunk 39 optimal weight: 5.9990 chunk 6 optimal weight: 0.9980 chunk 29 optimal weight: 9.9990 chunk 32 optimal weight: 7.9990 chunk 26 optimal weight: 0.8980 chunk 5 optimal weight: 4.9990 chunk 12 optimal weight: 8.9990 chunk 30 optimal weight: 0.7980 overall best weight: 1.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 65 ASN ** 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 = 0.4503 r_free = 0.4503 target = 0.148270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.122713 restraints weight = 11637.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.128962 restraints weight = 5698.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.133660 restraints weight = 3389.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4394 r_free = 0.4394 target = 0.137092 restraints weight = 2247.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4418 r_free = 0.4418 target = 0.139550 restraints weight = 1587.785| |-----------------------------------------------------------------------------| r_work (final): 0.4441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7389 moved from start: 0.8835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 3100 Z= 0.107 Angle : 0.555 5.174 4200 Z= 0.304 Chirality : 0.050 0.127 570 Planarity : 0.001 0.004 510 Dihedral : 6.269 19.995 440 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.90 % Favored : 88.10 % Rotamer: Outliers : 0.30 % Allowed : 20.00 % Favored : 79.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.36 (0.30), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.32 (0.23), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.006 0.001 TYR C 39 HIS 0.001 0.000 HIS E 50 Details of bonding type rmsd covalent geometry : bond 0.00210 ( 3100) covalent geometry : angle 0.55481 ( 4200) hydrogen bonds : bond 0.01501 ( 48) hydrogen bonds : angle 3.51774 ( 144) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1660.37 seconds wall clock time: 28 minutes 52.74 seconds (1732.74 seconds total)