Starting phenix.real_space_refine on Sat Apr 4 20:39:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9rb9_53888/04_2026/9rb9_53888.cif Found real_map, /net/cci-nas-00/data/ceres_data/9rb9_53888/04_2026/9rb9_53888.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9rb9_53888/04_2026/9rb9_53888.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9rb9_53888/04_2026/9rb9_53888.map" model { file = "/net/cci-nas-00/data/ceres_data/9rb9_53888/04_2026/9rb9_53888.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9rb9_53888/04_2026/9rb9_53888.cif" } resolution = 3.04 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= 0.006 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 1940 2.51 5 N 540 2.21 5 O 610 1.98 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: 3090 Number of models: 1 Model: "" Number of chains: 1 Chain: "C" Number of atoms: 309 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 309 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: 0.42, per 1000 atoms: 0.14 Number of scatterers: 3090 At special positions: 0 Unit cell: (57.368, 96.152, 38.784, 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 610 8.00 N 540 7.00 C 1940 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: 0.24 Conformation dependent library (CDL) restraints added in 186.8 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: 0.14 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 38 through 39 removed outlier: 7.070A pdb=" N LEU A 38 " --> pdb=" O TYR B 39 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N LEU C 38 " --> pdb=" O TYR D 39 " (cutoff:3.500A) removed outlier: 6.879A 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: 6.616A 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: 6.238A 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: 6.333A 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: 6.338A pdb=" N GLN D 62 " --> pdb=" O VAL E 63 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N ASN E 65 " --> pdb=" O GLN D 62 " (cutoff:3.500A) removed outlier: 6.494A 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: 6.234A pdb=" N THR A 75 " --> pdb=" O ALA B 76 " (cutoff:3.500A) removed outlier: 8.023A pdb=" N ALA B 78 " --> pdb=" O THR A 75 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N VAL A 77 " --> pdb=" O ALA B 78 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N THR C 75 " --> pdb=" O ALA D 76 " (cutoff:3.500A) removed outlier: 8.094A 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: 6.253A pdb=" N THR D 75 " --> pdb=" O ALA E 76 " (cutoff:3.500A) removed outlier: 8.058A pdb=" N ALA E 78 " --> pdb=" O THR D 75 " (cutoff:3.500A) removed outlier: 6.356A 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: 6.936A pdb=" N LEU G 38 " --> pdb=" O TYR H 39 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N LEU H 38 " --> pdb=" O TYR I 39 " (cutoff:3.500A) removed outlier: 6.893A 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 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: 6.271A pdb=" N THR G 54 " --> pdb=" O VAL H 55 " (cutoff:3.500A) removed outlier: 6.259A 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) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'F' and resid 61 through 65 removed outlier: 6.380A pdb=" N GLN G 62 " --> pdb=" O VAL H 63 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N ASN H 65 " --> pdb=" O GLN G 62 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N THR G 64 " --> pdb=" O ASN H 65 " (cutoff:3.500A) removed outlier: 6.393A 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: 6.556A 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: 6.269A pdb=" N THR F 75 " --> pdb=" O ALA G 76 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N ALA G 78 " --> pdb=" O THR F 75 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N VAL F 77 " --> pdb=" O ALA G 78 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N THR G 75 " --> pdb=" O ALA H 76 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N ALA H 78 " --> pdb=" O THR G 75 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N VAL G 77 " --> pdb=" O ALA H 78 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N THR H 75 " --> pdb=" O ALA I 76 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N ALA I 78 " --> pdb=" O THR H 75 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N VAL H 77 " --> pdb=" O ALA I 78 " (cutoff:3.500A) removed outlier: 6.265A 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: 6.364A 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: 0.32 Time building geometry restraints manager: 0.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.26: 530 1.26 - 1.35: 480 1.35 - 1.43: 120 1.43 - 1.51: 753 1.51 - 1.60: 1217 Bond restraints: 3100 Sorted by residual: bond pdb=" N VAL H 37 " pdb=" CA VAL H 37 " ideal model delta sigma weight residual 1.458 1.587 -0.129 1.90e-02 2.77e+03 4.60e+01 bond pdb=" N VAL D 37 " pdb=" CA VAL D 37 " ideal model delta sigma weight residual 1.458 1.587 -0.129 1.90e-02 2.77e+03 4.59e+01 bond pdb=" N VAL A 37 " pdb=" CA VAL A 37 " ideal model delta sigma weight residual 1.458 1.587 -0.129 1.90e-02 2.77e+03 4.59e+01 bond pdb=" N VAL F 37 " pdb=" CA VAL F 37 " ideal model delta sigma weight residual 1.458 1.587 -0.129 1.90e-02 2.77e+03 4.58e+01 bond pdb=" N VAL G 37 " pdb=" CA VAL G 37 " ideal model delta sigma weight residual 1.458 1.586 -0.128 1.90e-02 2.77e+03 4.57e+01 ... (remaining 3095 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.24: 3504 3.24 - 6.49: 566 6.49 - 9.73: 90 9.73 - 12.97: 20 12.97 - 16.22: 20 Bond angle restraints: 4200 Sorted by residual: angle pdb=" N GLY C 68 " pdb=" CA GLY C 68 " pdb=" C GLY C 68 " ideal model delta sigma weight residual 112.48 128.70 -16.22 1.21e+00 6.83e-01 1.80e+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 1.80e+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 1.80e+02 angle pdb=" N GLY F 68 " pdb=" CA GLY F 68 " pdb=" C GLY F 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 G 68 " pdb=" CA GLY G 68 " pdb=" C GLY G 68 " ideal model delta sigma weight residual 112.48 128.68 -16.20 1.21e+00 6.83e-01 1.79e+02 ... (remaining 4195 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 7.94: 1460 7.94 - 15.88: 240 15.88 - 23.81: 90 23.81 - 31.75: 10 31.75 - 39.69: 20 Dihedral angle restraints: 1820 sinusoidal: 620 harmonic: 1200 Sorted by residual: dihedral pdb=" C VAL J 52 " pdb=" N VAL J 52 " pdb=" CA VAL J 52 " pdb=" CB VAL J 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 H 52 " pdb=" N VAL H 52 " pdb=" CA VAL H 52 " pdb=" CB VAL H 52 " ideal model delta harmonic sigma weight residual -122.00 -112.33 -9.67 0 2.50e+00 1.60e-01 1.50e+01 ... (remaining 1817 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.106: 412 0.106 - 0.213: 118 0.213 - 0.319: 20 0.319 - 0.425: 10 0.425 - 0.531: 10 Chirality restraints: 570 Sorted by residual: chirality pdb=" CA ALA E 69 " pdb=" N ALA E 69 " pdb=" C ALA E 69 " pdb=" CB ALA E 69 " both_signs ideal model delta sigma weight residual False 2.48 1.95 0.53 2.00e-01 2.50e+01 7.06e+00 chirality pdb=" CA ALA C 69 " pdb=" N ALA C 69 " pdb=" C ALA C 69 " pdb=" CB ALA C 69 " both_signs ideal model delta sigma weight residual False 2.48 1.95 0.53 2.00e-01 2.50e+01 7.06e+00 chirality pdb=" CA ALA G 69 " pdb=" N ALA G 69 " pdb=" C ALA G 69 " pdb=" CB ALA G 69 " both_signs ideal model delta sigma weight residual False 2.48 1.95 0.53 2.00e-01 2.50e+01 7.03e+00 ... (remaining 567 not shown) Planarity restraints: 510 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR I 59 " -0.013 2.00e-02 2.50e+03 2.61e-02 6.83e+00 pdb=" C THR I 59 " 0.045 2.00e-02 2.50e+03 pdb=" O THR I 59 " -0.017 2.00e-02 2.50e+03 pdb=" N LYS I 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 2.60e-02 6.74e+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 D 59 " 0.013 2.00e-02 2.50e+03 2.59e-02 6.70e+00 pdb=" C THR D 59 " -0.045 2.00e-02 2.50e+03 pdb=" O THR D 59 " 0.017 2.00e-02 2.50e+03 pdb=" N LYS D 60 " 0.015 2.00e-02 2.50e+03 ... (remaining 507 not shown) Histogram of nonbonded interaction distances: 2.54 - 3.01: 1770 3.01 - 3.49: 2802 3.49 - 3.96: 4628 3.96 - 4.43: 5073 4.43 - 4.90: 10873 Nonbonded interactions: 25146 Sorted by model distance: nonbonded pdb=" N GLY I 51 " pdb=" O GLY I 51 " model vdw 2.544 2.496 nonbonded pdb=" N GLY A 51 " pdb=" O GLY A 51 " model vdw 2.544 2.496 nonbonded pdb=" N GLY G 51 " pdb=" O GLY G 51 " model vdw 2.544 2.496 nonbonded pdb=" N GLY D 51 " pdb=" O GLY D 51 " model vdw 2.544 2.496 nonbonded pdb=" N GLY C 51 " pdb=" O GLY C 51 " model vdw 2.544 2.496 ... (remaining 25141 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.050 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.650 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:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 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 : 2.747 16.217 4200 Z= 1.991 Chirality : 0.129 0.531 570 Planarity : 0.010 0.026 510 Dihedral : 10.298 39.686 1060 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 6.58 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 0.005 0.003 TYR J 39 HIS 0.002 0.001 HIS B 50 Details of bonding type rmsd covalent geometry : bond 0.02259 ( 3100) covalent geometry : angle 2.74748 ( 4200) hydrogen bonds : bond 0.14465 ( 48) hydrogen bonds : angle 5.29346 ( 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 139 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 129 time to evaluate : 0.117 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 0 residues processed: 139 average time/residue: 0.0523 time to fit residues: 9.0676 Evaluate side-chains 119 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 0.109 ------------------------------------------------------------------------------- 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: 1.9990 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 25 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 37 optimal weight: 5.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 79 GLN A 62 GLN A 79 GLN ** B 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 79 GLN D 62 GLN D 79 GLN E 65 ASN ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 79 GLN G 79 GLN H 79 GLN I 62 GLN I 79 GLN J 62 GLN J 65 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.123673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.108771 restraints weight = 3962.023| |-----------------------------------------------------------------------------| r_work (start): 0.3779 rms_B_bonded: 2.80 r_work: 0.3661 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work (final): 0.3661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.3363 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= 0.127 Angle : 0.560 4.528 4200 Z= 0.341 Chirality : 0.050 0.122 570 Planarity : 0.002 0.012 510 Dihedral : 7.090 21.761 440 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 5.76 % Allowed : 14.55 % 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: -2.55 (0.31), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.93 (0.24), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.017 0.003 TYR D 39 HIS 0.001 0.001 HIS E 50 Details of bonding type rmsd covalent geometry : bond 0.00275 ( 3100) covalent geometry : angle 0.55977 ( 4200) hydrogen bonds : bond 0.01748 ( 48) hydrogen bonds : angle 3.85115 ( 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 86 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 67 time to evaluate : 0.096 Fit side-chains revert: symmetry clash REVERT: A 61 GLU cc_start: 0.8532 (mt-10) cc_final: 0.8048 (mp0) REVERT: E 46 GLU cc_start: 0.8916 (tt0) cc_final: 0.8478 (tt0) REVERT: F 46 GLU cc_start: 0.8125 (mt-10) cc_final: 0.7884 (mt-10) REVERT: F 61 GLU cc_start: 0.8527 (mt-10) cc_final: 0.8028 (mp0) REVERT: G 46 GLU cc_start: 0.8239 (mt-10) cc_final: 0.7817 (mt-10) outliers start: 19 outliers final: 11 residues processed: 79 average time/residue: 0.0514 time to fit residues: 5.1069 Evaluate side-chains 76 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 65 time to evaluate : 0.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 54 THR Chi-restraints excluded: chain G residue 58 LYS Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain H residue 44 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 3 optimal weight: 6.9990 chunk 38 optimal weight: 10.0000 chunk 25 optimal weight: 8.9990 chunk 8 optimal weight: 10.0000 chunk 35 optimal weight: 8.9990 chunk 19 optimal weight: 8.9990 chunk 26 optimal weight: 7.9990 chunk 34 optimal weight: 2.9990 chunk 28 optimal weight: 9.9990 chunk 9 optimal weight: 6.9990 chunk 13 optimal weight: 1.9990 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 79 GLN D 79 GLN F 79 GLN G 79 GLN ** H 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 79 GLN I 65 ASN I 79 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.105850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.091192 restraints weight = 4157.054| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 2.73 r_work: 0.3387 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3269 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.3756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.035 3100 Z= 0.342 Angle : 0.655 3.057 4200 Z= 0.399 Chirality : 0.054 0.121 570 Planarity : 0.003 0.014 510 Dihedral : 7.929 24.803 440 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.62 % Favored : 92.38 % Rotamer: Outliers : 7.27 % Allowed : 13.94 % Favored : 78.79 % 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: -2.65 (0.33), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.01 (0.25), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.008 0.002 TYR D 39 HIS 0.003 0.001 HIS F 50 Details of bonding type rmsd covalent geometry : bond 0.00790 ( 3100) covalent geometry : angle 0.65507 ( 4200) hydrogen bonds : bond 0.02457 ( 48) hydrogen bonds : angle 4.07669 ( 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 93 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 69 time to evaluate : 0.108 Fit side-chains REVERT: C 80 LYS cc_start: 0.7871 (mttp) cc_final: 0.7337 (mtpt) REVERT: A 80 LYS cc_start: 0.8408 (mttp) cc_final: 0.7464 (mtpt) REVERT: B 75 THR cc_start: 0.8660 (OUTLIER) cc_final: 0.8442 (m) REVERT: B 80 LYS cc_start: 0.7929 (mttp) cc_final: 0.7060 (mtpt) REVERT: D 80 LYS cc_start: 0.7921 (mttp) cc_final: 0.7348 (mtpt) REVERT: E 46 GLU cc_start: 0.8875 (tt0) cc_final: 0.8457 (tt0) REVERT: E 80 LYS cc_start: 0.7817 (mttp) cc_final: 0.6977 (mtpt) REVERT: F 80 LYS cc_start: 0.8365 (mttp) cc_final: 0.7431 (mtpt) REVERT: G 46 GLU cc_start: 0.8456 (mt-10) cc_final: 0.8031 (mt-10) REVERT: G 58 LYS cc_start: 0.8303 (OUTLIER) cc_final: 0.8035 (tptp) REVERT: G 80 LYS cc_start: 0.7972 (mttp) cc_final: 0.7115 (mtpt) REVERT: H 46 GLU cc_start: 0.8540 (mt-10) cc_final: 0.8091 (tt0) REVERT: H 80 LYS cc_start: 0.7906 (mttp) cc_final: 0.7268 (mtpt) REVERT: I 46 GLU cc_start: 0.8521 (mt-10) cc_final: 0.8185 (tt0) REVERT: I 80 LYS cc_start: 0.7930 (mttp) cc_final: 0.7244 (mtpt) REVERT: J 46 GLU cc_start: 0.8771 (mt-10) cc_final: 0.8490 (tt0) REVERT: J 80 LYS cc_start: 0.7997 (mttp) cc_final: 0.7184 (mtpt) outliers start: 24 outliers final: 20 residues processed: 81 average time/residue: 0.0758 time to fit residues: 7.1657 Evaluate side-chains 90 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 68 time to evaluate : 0.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 58 LYS Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 54 THR Chi-restraints excluded: chain G residue 58 LYS Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 54 THR Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain J residue 54 THR Chi-restraints excluded: chain J residue 75 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 8 optimal weight: 3.9990 chunk 2 optimal weight: 0.9990 chunk 36 optimal weight: 5.9990 chunk 3 optimal weight: 6.9990 chunk 29 optimal weight: 6.9990 chunk 30 optimal weight: 0.6980 chunk 35 optimal weight: 6.9990 chunk 15 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 79 GLN D 79 GLN E 79 GLN I 79 GLN J 79 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.116455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.101597 restraints weight = 3892.340| |-----------------------------------------------------------------------------| r_work (start): 0.3693 rms_B_bonded: 2.78 r_work: 0.3548 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3414 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.4080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 3100 Z= 0.111 Angle : 0.479 3.080 4200 Z= 0.288 Chirality : 0.049 0.118 570 Planarity : 0.002 0.011 510 Dihedral : 6.359 19.275 440 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 4.85 % Allowed : 16.97 % Favored : 78.18 % 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: -2.10 (0.36), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.59 (0.28), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.010 0.002 TYR D 39 HIS 0.002 0.001 HIS C 50 Details of bonding type rmsd covalent geometry : bond 0.00240 ( 3100) covalent geometry : angle 0.47864 ( 4200) hydrogen bonds : bond 0.01833 ( 48) hydrogen bonds : angle 3.75171 ( 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 88 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 72 time to evaluate : 0.122 Fit side-chains revert: symmetry clash REVERT: C 80 LYS cc_start: 0.7789 (mttp) cc_final: 0.7115 (mtpt) REVERT: A 46 GLU cc_start: 0.8544 (mt-10) cc_final: 0.8284 (tt0) REVERT: A 80 LYS cc_start: 0.8304 (mttp) cc_final: 0.7601 (mtpt) REVERT: B 80 LYS cc_start: 0.7829 (mttp) cc_final: 0.7195 (mtpt) REVERT: D 80 LYS cc_start: 0.7819 (mttp) cc_final: 0.7227 (mtpt) REVERT: E 46 GLU cc_start: 0.8613 (tt0) cc_final: 0.8186 (tt0) REVERT: E 80 LYS cc_start: 0.7928 (mttp) cc_final: 0.7074 (mtpt) REVERT: F 46 GLU cc_start: 0.8297 (mt-10) cc_final: 0.7966 (mt-10) REVERT: F 80 LYS cc_start: 0.8270 (mttp) cc_final: 0.7590 (mtpt) REVERT: G 46 GLU cc_start: 0.8411 (mt-10) cc_final: 0.8073 (mt-10) REVERT: G 80 LYS cc_start: 0.7916 (mttp) cc_final: 0.6984 (mtpt) REVERT: H 46 GLU cc_start: 0.8368 (mt-10) cc_final: 0.7991 (tt0) REVERT: H 80 LYS cc_start: 0.7886 (mttp) cc_final: 0.7105 (mtpt) REVERT: I 46 GLU cc_start: 0.8446 (mt-10) cc_final: 0.8072 (tt0) REVERT: I 80 LYS cc_start: 0.7871 (mttp) cc_final: 0.7201 (mtpt) REVERT: J 46 GLU cc_start: 0.8652 (OUTLIER) cc_final: 0.8371 (tt0) REVERT: J 80 LYS cc_start: 0.8019 (mttp) cc_final: 0.7129 (mtpt) outliers start: 16 outliers final: 11 residues processed: 79 average time/residue: 0.0745 time to fit residues: 6.9122 Evaluate side-chains 84 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 72 time to evaluate : 0.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 54 THR Chi-restraints excluded: chain G residue 58 LYS Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 54 THR Chi-restraints excluded: chain J residue 46 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 3 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 13 optimal weight: 9.9990 chunk 27 optimal weight: 9.9990 chunk 29 optimal weight: 4.9990 chunk 37 optimal weight: 9.9990 chunk 8 optimal weight: 9.9990 chunk 24 optimal weight: 10.0000 chunk 2 optimal weight: 5.9990 chunk 35 optimal weight: 7.9990 chunk 0 optimal weight: 7.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 79 GLN D 79 GLN E 79 GLN I 79 GLN J 79 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.105002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.090760 restraints weight = 4080.373| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 2.70 r_work: 0.3366 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3246 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.4099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.027 3100 Z= 0.284 Angle : 0.564 3.344 4200 Z= 0.345 Chirality : 0.051 0.120 570 Planarity : 0.002 0.011 510 Dihedral : 7.169 22.635 440 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.14 % Favored : 87.86 % Rotamer: Outliers : 6.06 % Allowed : 15.15 % Favored : 78.79 % 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: -2.45 (0.34), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.86 (0.26), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.007 0.002 TYR D 39 HIS 0.003 0.001 HIS D 50 Details of bonding type rmsd covalent geometry : bond 0.00644 ( 3100) covalent geometry : angle 0.56414 ( 4200) hydrogen bonds : bond 0.02135 ( 48) hydrogen bonds : angle 3.88626 ( 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 84 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 64 time to evaluate : 0.120 Fit side-chains REVERT: C 80 LYS cc_start: 0.7956 (mttp) cc_final: 0.7182 (mtpt) REVERT: D 80 LYS cc_start: 0.7936 (mttp) cc_final: 0.7045 (mtpt) REVERT: E 46 GLU cc_start: 0.8730 (tt0) cc_final: 0.8324 (tt0) REVERT: E 80 LYS cc_start: 0.7996 (mttp) cc_final: 0.7129 (mtpt) REVERT: F 46 GLU cc_start: 0.8291 (mt-10) cc_final: 0.8019 (mt-10) REVERT: G 46 GLU cc_start: 0.8363 (mt-10) cc_final: 0.8041 (mt-10) REVERT: G 58 LYS cc_start: 0.8239 (OUTLIER) cc_final: 0.7919 (tptp) REVERT: H 46 GLU cc_start: 0.8368 (mt-10) cc_final: 0.8026 (tt0) REVERT: H 80 LYS cc_start: 0.7998 (mttp) cc_final: 0.7144 (mtpt) REVERT: I 46 GLU cc_start: 0.8456 (mt-10) cc_final: 0.8226 (tt0) REVERT: I 79 GLN cc_start: 0.8450 (tt0) cc_final: 0.8243 (tt0) REVERT: I 80 LYS cc_start: 0.7986 (mttp) cc_final: 0.6986 (mtpt) REVERT: J 46 GLU cc_start: 0.8639 (OUTLIER) cc_final: 0.8347 (tt0) REVERT: J 80 LYS cc_start: 0.8014 (mttp) cc_final: 0.7119 (mtpt) outliers start: 20 outliers final: 16 residues processed: 72 average time/residue: 0.0781 time to fit residues: 6.6576 Evaluate side-chains 82 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 64 time to evaluate : 0.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 54 THR Chi-restraints excluded: chain G residue 58 LYS Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 54 THR Chi-restraints excluded: chain H residue 58 LYS Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain J residue 46 GLU Chi-restraints excluded: chain J residue 54 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 29 optimal weight: 3.9990 chunk 4 optimal weight: 10.0000 chunk 1 optimal weight: 7.9990 chunk 31 optimal weight: 8.9990 chunk 8 optimal weight: 2.9990 chunk 22 optimal weight: 7.9990 chunk 27 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 39 optimal weight: 7.9990 chunk 38 optimal weight: 2.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 79 GLN D 79 GLN E 79 GLN J 79 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.112989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.098644 restraints weight = 3840.605| |-----------------------------------------------------------------------------| r_work (start): 0.3598 rms_B_bonded: 2.62 r_work: 0.3480 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3355 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.4256 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= 0.141 Angle : 0.500 3.833 4200 Z= 0.298 Chirality : 0.049 0.119 570 Planarity : 0.002 0.013 510 Dihedral : 6.281 19.300 440 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 6.06 % Allowed : 13.94 % 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: -2.16 (0.36), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.63 (0.27), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.010 0.002 TYR A 39 HIS 0.002 0.001 HIS E 50 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 3100) covalent geometry : angle 0.49982 ( 4200) hydrogen bonds : bond 0.01735 ( 48) hydrogen bonds : angle 3.71468 ( 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 80 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 60 time to evaluate : 0.119 Fit side-chains revert: symmetry clash REVERT: C 80 LYS cc_start: 0.7846 (mttp) cc_final: 0.6942 (mtpt) REVERT: B 58 LYS cc_start: 0.8524 (OUTLIER) cc_final: 0.8125 (tptp) REVERT: D 80 LYS cc_start: 0.8018 (mttp) cc_final: 0.7100 (mtpt) REVERT: E 46 GLU cc_start: 0.8555 (tt0) cc_final: 0.8179 (tt0) REVERT: F 46 GLU cc_start: 0.8285 (mt-10) cc_final: 0.7863 (mt-10) REVERT: G 46 GLU cc_start: 0.8274 (mt-10) cc_final: 0.7878 (mt-10) REVERT: H 46 GLU cc_start: 0.8228 (mt-10) cc_final: 0.7889 (tt0) REVERT: I 46 GLU cc_start: 0.8362 (mt-10) cc_final: 0.7990 (tt0) REVERT: I 80 LYS cc_start: 0.8027 (mttp) cc_final: 0.7028 (mtpt) REVERT: J 46 GLU cc_start: 0.8570 (OUTLIER) cc_final: 0.8306 (tt0) outliers start: 20 outliers final: 16 residues processed: 66 average time/residue: 0.0723 time to fit residues: 5.7061 Evaluate side-chains 78 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 60 time to evaluate : 0.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 58 LYS Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 54 THR Chi-restraints excluded: chain G residue 58 LYS Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 54 THR Chi-restraints excluded: chain H residue 58 LYS Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain J residue 46 GLU Chi-restraints excluded: chain J residue 54 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 25 optimal weight: 8.9990 chunk 26 optimal weight: 4.9990 chunk 20 optimal weight: 10.0000 chunk 16 optimal weight: 2.9990 chunk 28 optimal weight: 10.0000 chunk 22 optimal weight: 0.7980 chunk 36 optimal weight: 4.9990 chunk 7 optimal weight: 5.9990 chunk 21 optimal weight: 2.9990 chunk 24 optimal weight: 5.9990 chunk 12 optimal weight: 3.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 79 GLN D 79 GLN E 79 GLN I 79 GLN J 79 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.109230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.095140 restraints weight = 3884.634| |-----------------------------------------------------------------------------| r_work (start): 0.3533 rms_B_bonded: 2.57 r_work: 0.3416 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3296 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.4263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.022 3100 Z= 0.210 Angle : 0.516 3.217 4200 Z= 0.312 Chirality : 0.049 0.123 570 Planarity : 0.002 0.011 510 Dihedral : 6.567 20.355 440 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.76 % Favored : 85.24 % Rotamer: Outliers : 6.06 % Allowed : 13.94 % 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: -2.24 (0.35), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.70 (0.27), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.008 0.002 TYR A 39 HIS 0.002 0.001 HIS J 50 Details of bonding type rmsd covalent geometry : bond 0.00469 ( 3100) covalent geometry : angle 0.51632 ( 4200) hydrogen bonds : bond 0.01832 ( 48) hydrogen bonds : angle 3.79695 ( 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 73 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 53 time to evaluate : 0.124 Fit side-chains REVERT: E 46 GLU cc_start: 0.8572 (tt0) cc_final: 0.8167 (tt0) REVERT: F 46 GLU cc_start: 0.8236 (mt-10) cc_final: 0.7987 (mt-10) REVERT: G 46 GLU cc_start: 0.8238 (mt-10) cc_final: 0.7949 (mt-10) REVERT: H 46 GLU cc_start: 0.8232 (mt-10) cc_final: 0.7962 (tt0) REVERT: I 46 GLU cc_start: 0.8339 (mt-10) cc_final: 0.8036 (tt0) REVERT: J 46 GLU cc_start: 0.8610 (OUTLIER) cc_final: 0.8361 (tt0) outliers start: 20 outliers final: 15 residues processed: 61 average time/residue: 0.0617 time to fit residues: 4.6216 Evaluate side-chains 69 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 53 time to evaluate : 0.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 54 THR Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 54 THR Chi-restraints excluded: chain H residue 58 LYS Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain J residue 46 GLU Chi-restraints excluded: chain J residue 54 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 1 optimal weight: 10.0000 chunk 11 optimal weight: 0.9990 chunk 26 optimal weight: 4.9990 chunk 22 optimal weight: 0.6980 chunk 23 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 3 optimal weight: 1.9990 chunk 15 optimal weight: 4.9990 chunk 17 optimal weight: 5.9990 chunk 9 optimal weight: 5.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 79 GLN E 79 GLN J 79 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.112990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.098497 restraints weight = 3857.590| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 2.63 r_work: 0.3450 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3319 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.4371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.016 3100 Z= 0.139 Angle : 0.495 3.736 4200 Z= 0.293 Chirality : 0.048 0.119 570 Planarity : 0.002 0.015 510 Dihedral : 6.113 18.364 440 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.48 % Favored : 89.52 % Rotamer: Outliers : 5.15 % Allowed : 15.15 % 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: -2.01 (0.36), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.52 (0.28), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.010 0.002 TYR A 39 HIS 0.002 0.001 HIS A 50 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 3100) covalent geometry : angle 0.49479 ( 4200) hydrogen bonds : bond 0.01646 ( 48) hydrogen bonds : angle 3.68886 ( 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 71 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 54 time to evaluate : 0.115 Fit side-chains REVERT: E 46 GLU cc_start: 0.8566 (tt0) cc_final: 0.8133 (tt0) REVERT: F 46 GLU cc_start: 0.8295 (mt-10) cc_final: 0.8015 (mt-10) REVERT: G 46 GLU cc_start: 0.8240 (mt-10) cc_final: 0.7804 (mt-10) REVERT: H 46 GLU cc_start: 0.8238 (mt-10) cc_final: 0.7869 (tt0) REVERT: I 46 GLU cc_start: 0.8338 (mt-10) cc_final: 0.7984 (tt0) REVERT: J 46 GLU cc_start: 0.8583 (OUTLIER) cc_final: 0.8322 (tt0) outliers start: 17 outliers final: 15 residues processed: 60 average time/residue: 0.0609 time to fit residues: 4.4976 Evaluate side-chains 69 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 53 time to evaluate : 0.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 54 THR Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 54 THR Chi-restraints excluded: chain H residue 58 LYS Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain J residue 46 GLU Chi-restraints excluded: chain J residue 54 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 39 optimal weight: 0.3980 chunk 32 optimal weight: 4.9990 chunk 19 optimal weight: 9.9990 chunk 37 optimal weight: 1.9990 chunk 4 optimal weight: 10.0000 chunk 28 optimal weight: 3.9990 chunk 1 optimal weight: 10.0000 chunk 14 optimal weight: 7.9990 chunk 29 optimal weight: 8.9990 chunk 9 optimal weight: 3.9990 chunk 10 optimal weight: 8.9990 overall best weight: 3.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 79 GLN E 79 GLN J 79 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.107347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.093112 restraints weight = 4064.963| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 2.69 r_work: 0.3410 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3287 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.4342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.020 3100 Z= 0.205 Angle : 0.516 3.893 4200 Z= 0.311 Chirality : 0.049 0.123 570 Planarity : 0.002 0.013 510 Dihedral : 6.470 20.131 440 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.71 % Favored : 84.29 % Rotamer: Outliers : 5.15 % Allowed : 15.45 % 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: -2.16 (0.35), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.64 (0.27), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.008 0.002 TYR A 39 HIS 0.002 0.001 HIS J 50 Details of bonding type rmsd covalent geometry : bond 0.00457 ( 3100) covalent geometry : angle 0.51629 ( 4200) hydrogen bonds : bond 0.01776 ( 48) hydrogen bonds : angle 3.75248 ( 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 73 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 56 time to evaluate : 0.104 Fit side-chains REVERT: E 46 GLU cc_start: 0.8541 (tt0) cc_final: 0.8081 (tt0) REVERT: F 46 GLU cc_start: 0.8282 (mt-10) cc_final: 0.7905 (mt-10) REVERT: G 46 GLU cc_start: 0.8187 (mt-10) cc_final: 0.7840 (mt-10) REVERT: H 46 GLU cc_start: 0.8195 (mt-10) cc_final: 0.7899 (tt0) REVERT: I 46 GLU cc_start: 0.8317 (mt-10) cc_final: 0.7986 (tt0) REVERT: J 46 GLU cc_start: 0.8607 (mt-10) cc_final: 0.8329 (tt0) outliers start: 17 outliers final: 15 residues processed: 63 average time/residue: 0.0583 time to fit residues: 4.5222 Evaluate side-chains 71 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 56 time to evaluate : 0.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 54 THR Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 54 THR Chi-restraints excluded: chain H residue 58 LYS Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain J residue 54 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 23 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 9 optimal weight: 6.9990 chunk 5 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 20 optimal weight: 10.0000 chunk 10 optimal weight: 4.9990 chunk 4 optimal weight: 8.9990 chunk 37 optimal weight: 6.9990 chunk 21 optimal weight: 5.9990 chunk 29 optimal weight: 6.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 79 GLN E 79 GLN J 79 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.103689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.089733 restraints weight = 4070.512| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 2.63 r_work: 0.3343 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3221 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.4320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.029 3100 Z= 0.306 Angle : 0.594 4.114 4200 Z= 0.362 Chirality : 0.052 0.128 570 Planarity : 0.003 0.014 510 Dihedral : 6.973 21.242 440 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.38 % Favored : 82.62 % Rotamer: Outliers : 4.55 % Allowed : 15.76 % 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: -2.60 (0.33), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.98 (0.25), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.007 0.002 TYR D 39 HIS 0.003 0.002 HIS J 50 Details of bonding type rmsd covalent geometry : bond 0.00696 ( 3100) covalent geometry : angle 0.59416 ( 4200) hydrogen bonds : bond 0.02081 ( 48) hydrogen bonds : angle 3.81417 ( 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 77 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 62 time to evaluate : 0.121 Fit side-chains REVERT: E 46 GLU cc_start: 0.8659 (tt0) cc_final: 0.8223 (tt0) REVERT: F 46 GLU cc_start: 0.8345 (mt-10) cc_final: 0.7979 (mt-10) REVERT: G 46 GLU cc_start: 0.8297 (mt-10) cc_final: 0.7954 (mt-10) REVERT: H 46 GLU cc_start: 0.8227 (mt-10) cc_final: 0.7957 (tt0) REVERT: I 46 GLU cc_start: 0.8340 (mt-10) cc_final: 0.8068 (tt0) REVERT: J 46 GLU cc_start: 0.8581 (OUTLIER) cc_final: 0.8276 (tt0) outliers start: 15 outliers final: 13 residues processed: 65 average time/residue: 0.0602 time to fit residues: 4.8243 Evaluate side-chains 76 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 62 time to evaluate : 0.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain A residue 65 ASN Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain G residue 54 THR Chi-restraints excluded: chain H residue 54 THR Chi-restraints excluded: chain H residue 58 LYS Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain J residue 46 GLU Chi-restraints excluded: chain J residue 54 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 7 optimal weight: 4.9990 chunk 39 optimal weight: 6.9990 chunk 1 optimal weight: 4.9990 chunk 33 optimal weight: 5.9990 chunk 23 optimal weight: 7.9990 chunk 4 optimal weight: 10.0000 chunk 34 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 79 GLN E 79 GLN J 79 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.108535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.094034 restraints weight = 4092.188| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 2.75 r_work: 0.3418 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3283 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.4393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.019 3100 Z= 0.164 Angle : 0.511 4.731 4200 Z= 0.305 Chirality : 0.049 0.119 570 Planarity : 0.002 0.012 510 Dihedral : 6.274 19.232 440 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.05 % Favored : 85.95 % Rotamer: Outliers : 3.64 % Allowed : 16.67 % 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: -2.24 (0.35), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.70 (0.27), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.009 0.002 TYR A 39 HIS 0.002 0.001 HIS F 50 Details of bonding type rmsd covalent geometry : bond 0.00362 ( 3100) covalent geometry : angle 0.51114 ( 4200) hydrogen bonds : bond 0.01682 ( 48) hydrogen bonds : angle 3.72145 ( 144) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 874.25 seconds wall clock time: 15 minutes 39.78 seconds (939.78 seconds total)