Starting phenix.real_space_refine on Fri Aug 22 14:10:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x7q_38107/08_2025/8x7q_38107.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x7q_38107/08_2025/8x7q_38107.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8x7q_38107/08_2025/8x7q_38107.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x7q_38107/08_2025/8x7q_38107.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8x7q_38107/08_2025/8x7q_38107.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x7q_38107/08_2025/8x7q_38107.map" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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 S 20 5.16 5 C 2454 2.51 5 N 680 2.21 5 O 782 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-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3936 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 378 Classifications: {'peptide': 55} Link IDs: {'CIS': 3, 'TRANS': 51} Chain: "B" Number of atoms: 378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 378 Classifications: {'peptide': 55} Link IDs: {'CIS': 3, 'TRANS': 51} Chain: "C" Number of atoms: 378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 378 Classifications: {'peptide': 55} Link IDs: {'CIS': 3, 'TRANS': 51} Chain: "D" Number of atoms: 378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 378 Classifications: {'peptide': 55} Link IDs: {'CIS': 3, 'TRANS': 51} Chain: "E" Number of atoms: 378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 378 Classifications: {'peptide': 55} Link IDs: {'CIS': 3, 'TRANS': 51} Chain: "F" Number of atoms: 378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 378 Classifications: {'peptide': 55} Link IDs: {'CIS': 3, 'TRANS': 51} Chain: "G" Number of atoms: 378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 378 Classifications: {'peptide': 55} Link IDs: {'CIS': 3, 'TRANS': 51} Chain: "H" Number of atoms: 378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 378 Classifications: {'peptide': 55} Link IDs: {'CIS': 3, 'TRANS': 51} Chain: "I" Number of atoms: 378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 378 Classifications: {'peptide': 55} Link IDs: {'CIS': 3, 'TRANS': 51} Chain: "J" Number of atoms: 378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 378 Classifications: {'peptide': 55} Link IDs: {'CIS': 3, 'TRANS': 51} Chain: "A" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 39 Unusual residues: {'3LS': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 39 Unusual residues: {'3LS': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 39 Unusual residues: {'3LS': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 39 Unusual residues: {'3LS': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.08, per 1000 atoms: 0.27 Number of scatterers: 3936 At special positions: 0 Unit cell: (74.7, 110.39, 44.82, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 20 16.00 O 782 8.00 N 680 7.00 C 2454 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: 0.32 Conformation dependent library (CDL) restraints added in 157.0 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 940 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 10 sheets defined 0.0% alpha, 20.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'B' and resid 46 through 48 removed outlier: 6.725A pdb=" N GLY A 47 " --> pdb=" O VAL B 48 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N GLY I 47 " --> pdb=" O VAL J 48 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 63 through 64 removed outlier: 6.421A pdb=" N VAL A 63 " --> pdb=" O THR B 64 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N VAL I 63 " --> pdb=" O THR J 64 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 69 through 71 removed outlier: 6.511A pdb=" N VAL A 70 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N VAL I 70 " --> pdb=" O VAL J 71 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 75 through 78 removed outlier: 6.361A pdb=" N ALA A 76 " --> pdb=" O VAL B 77 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N THR E 75 " --> pdb=" O ALA J 76 " (cutoff:3.500A) removed outlier: 7.873A pdb=" N ALA J 78 " --> pdb=" O THR E 75 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N VAL E 77 " --> pdb=" O ALA J 78 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N ALA I 76 " --> pdb=" O VAL J 77 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 90 through 93 removed outlier: 8.873A pdb=" N ALA A 90 " --> pdb=" O ALA B 91 " (cutoff:3.500A) removed outlier: 9.034A pdb=" N GLY B 93 " --> pdb=" O ALA A 90 " (cutoff:3.500A) removed outlier: 5.297A pdb=" N THR A 92 " --> pdb=" O GLY B 93 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ALA A 91 " --> pdb=" O ALA E 90 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N THR E 92 " --> pdb=" O ALA A 91 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N ALA E 91 " --> pdb=" O ALA J 90 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N THR J 92 " --> pdb=" O ALA E 91 " (cutoff:3.500A) removed outlier: 8.850A pdb=" N ALA I 90 " --> pdb=" O ALA J 91 " (cutoff:3.500A) removed outlier: 9.012A pdb=" N GLY J 93 " --> pdb=" O ALA I 90 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N THR I 92 " --> pdb=" O GLY J 93 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 46 through 48 removed outlier: 6.724A pdb=" N GLY C 47 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N GLY F 47 " --> pdb=" O VAL G 48 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 63 through 64 removed outlier: 6.421A pdb=" N VAL C 63 " --> pdb=" O THR D 64 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N VAL F 63 " --> pdb=" O THR G 64 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 69 through 71 removed outlier: 6.511A pdb=" N VAL C 70 " --> pdb=" O VAL D 71 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N VAL F 70 " --> pdb=" O VAL G 71 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 75 through 78 removed outlier: 6.361A pdb=" N ALA C 76 " --> pdb=" O VAL D 77 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N ALA F 76 " --> pdb=" O VAL G 77 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 90 through 93 removed outlier: 8.874A pdb=" N ALA C 90 " --> pdb=" O ALA D 91 " (cutoff:3.500A) removed outlier: 9.033A pdb=" N GLY D 93 " --> pdb=" O ALA C 90 " (cutoff:3.500A) removed outlier: 5.297A pdb=" N THR C 92 " --> pdb=" O GLY D 93 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ALA C 91 " --> pdb=" O ALA G 90 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N THR G 92 " --> pdb=" O ALA C 91 " (cutoff:3.500A) removed outlier: 8.922A pdb=" N ALA F 90 " --> pdb=" O ALA G 91 " (cutoff:3.500A) removed outlier: 9.083A pdb=" N GLY G 93 " --> pdb=" O ALA F 90 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N THR F 92 " --> pdb=" O GLY G 93 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ALA F 91 " --> pdb=" O ALA H 90 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N THR H 92 " --> pdb=" O ALA F 91 " (cutoff:3.500A) 33 hydrogen bonds defined for protein. 99 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: 0.59 Time building geometry restraints manager: 0.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.31: 721 1.31 - 1.42: 757 1.42 - 1.52: 1796 1.52 - 1.62: 648 1.62 - 1.73: 40 Bond restraints: 3962 Sorted by residual: bond pdb=" CAI 3LS D 201 " pdb=" CAJ 3LS D 201 " ideal model delta sigma weight residual 1.446 1.385 0.061 2.00e-02 2.50e+03 9.33e+00 bond pdb=" CAI 3LS B 201 " pdb=" CAJ 3LS B 201 " ideal model delta sigma weight residual 1.446 1.385 0.061 2.00e-02 2.50e+03 9.27e+00 bond pdb=" CAF 3LS A 201 " pdb=" CAG 3LS A 201 " ideal model delta sigma weight residual 1.444 1.384 0.060 2.00e-02 2.50e+03 8.99e+00 bond pdb=" CAF 3LS B 201 " pdb=" CAG 3LS B 201 " ideal model delta sigma weight residual 1.444 1.384 0.060 2.00e-02 2.50e+03 8.99e+00 bond pdb=" CAF 3LS C 201 " pdb=" CAG 3LS C 201 " ideal model delta sigma weight residual 1.444 1.384 0.060 2.00e-02 2.50e+03 8.98e+00 ... (remaining 3957 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.76: 4537 1.76 - 3.51: 537 3.51 - 5.27: 215 5.27 - 7.02: 41 7.02 - 8.78: 32 Bond angle restraints: 5362 Sorted by residual: angle pdb=" N ILE A 88 " pdb=" CA ILE A 88 " pdb=" C ILE A 88 " ideal model delta sigma weight residual 108.12 103.41 4.71 1.34e+00 5.57e-01 1.24e+01 angle pdb=" N ILE G 88 " pdb=" CA ILE G 88 " pdb=" C ILE G 88 " ideal model delta sigma weight residual 108.12 103.43 4.69 1.34e+00 5.57e-01 1.22e+01 angle pdb=" N ILE D 88 " pdb=" CA ILE D 88 " pdb=" C ILE D 88 " ideal model delta sigma weight residual 108.12 103.44 4.68 1.34e+00 5.57e-01 1.22e+01 angle pdb=" N ILE B 88 " pdb=" CA ILE B 88 " pdb=" C ILE B 88 " ideal model delta sigma weight residual 108.12 103.45 4.67 1.34e+00 5.57e-01 1.21e+01 angle pdb=" N ILE C 88 " pdb=" CA ILE C 88 " pdb=" C ILE C 88 " ideal model delta sigma weight residual 108.12 103.45 4.67 1.34e+00 5.57e-01 1.21e+01 ... (remaining 5357 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 2101 17.89 - 35.77: 145 35.77 - 53.66: 42 53.66 - 71.54: 0 71.54 - 89.43: 8 Dihedral angle restraints: 2296 sinusoidal: 816 harmonic: 1480 Sorted by residual: dihedral pdb=" CA GLY I 67 " pdb=" C GLY I 67 " pdb=" N GLY I 68 " pdb=" CA GLY I 68 " ideal model delta harmonic sigma weight residual 0.00 25.12 -25.12 0 5.00e+00 4.00e-02 2.52e+01 dihedral pdb=" CA GLY A 67 " pdb=" C GLY A 67 " pdb=" N GLY A 68 " pdb=" CA GLY A 68 " ideal model delta harmonic sigma weight residual 0.00 25.10 -25.10 0 5.00e+00 4.00e-02 2.52e+01 dihedral pdb=" CA GLY J 67 " pdb=" C GLY J 67 " pdb=" N GLY J 68 " pdb=" CA GLY J 68 " ideal model delta harmonic sigma weight residual 0.00 25.07 -25.07 0 5.00e+00 4.00e-02 2.51e+01 ... (remaining 2293 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 365 0.052 - 0.105: 168 0.105 - 0.157: 97 0.157 - 0.210: 20 0.210 - 0.262: 20 Chirality restraints: 670 Sorted by residual: chirality pdb=" CA ILE B 88 " pdb=" N ILE B 88 " pdb=" C ILE B 88 " pdb=" CB ILE B 88 " both_signs ideal model delta sigma weight residual False 2.43 2.70 -0.26 2.00e-01 2.50e+01 1.72e+00 chirality pdb=" CA ILE G 88 " pdb=" N ILE G 88 " pdb=" C ILE G 88 " pdb=" CB ILE G 88 " both_signs ideal model delta sigma weight residual False 2.43 2.69 -0.26 2.00e-01 2.50e+01 1.68e+00 chirality pdb=" CA ILE H 88 " pdb=" N ILE H 88 " pdb=" C ILE H 88 " pdb=" CB ILE H 88 " both_signs ideal model delta sigma weight residual False 2.43 2.69 -0.26 2.00e-01 2.50e+01 1.68e+00 ... (remaining 667 not shown) Planarity restraints: 676 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL B 52 " -0.011 2.00e-02 2.50e+03 2.24e-02 5.00e+00 pdb=" C VAL B 52 " 0.039 2.00e-02 2.50e+03 pdb=" O VAL B 52 " -0.015 2.00e-02 2.50e+03 pdb=" N ALA B 53 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL I 52 " -0.011 2.00e-02 2.50e+03 2.24e-02 5.00e+00 pdb=" C VAL I 52 " 0.039 2.00e-02 2.50e+03 pdb=" O VAL I 52 " -0.015 2.00e-02 2.50e+03 pdb=" N ALA I 53 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL G 52 " 0.011 2.00e-02 2.50e+03 2.23e-02 4.99e+00 pdb=" C VAL G 52 " -0.039 2.00e-02 2.50e+03 pdb=" O VAL G 52 " 0.015 2.00e-02 2.50e+03 pdb=" N ALA G 53 " 0.013 2.00e-02 2.50e+03 ... (remaining 673 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 897 2.80 - 3.32: 3206 3.32 - 3.85: 6134 3.85 - 4.37: 7070 4.37 - 4.90: 14220 Nonbonded interactions: 31527 Sorted by model distance: nonbonded pdb=" O GLY A 86 " pdb=" CBE 3LS A 201 " model vdw 2.275 3.260 nonbonded pdb=" O GLY B 86 " pdb=" OAT 3LS A 201 " model vdw 2.276 3.040 nonbonded pdb=" CG1 VAL B 66 " pdb=" CBE 3LS B 201 " model vdw 2.372 3.680 nonbonded pdb=" CG1 VAL A 66 " pdb=" CBB 3LS B 201 " model vdw 2.421 3.680 nonbonded pdb=" OG1 THR F 64 " pdb=" OG1 THR H 54 " model vdw 2.513 3.040 ... (remaining 31522 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 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } ncs_group { reference = 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: 1.060 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: 0.080 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 5.760 Find NCS groups from input model: 0.040 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:6.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2318 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 : 0.014 0.072 3962 Z= 0.666 Angle : 1.603 8.775 5362 Z= 0.820 Chirality : 0.081 0.262 670 Planarity : 0.006 0.022 676 Dihedral : 14.718 89.428 1356 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 17.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.43 % Favored : 90.57 % Rotamer: Outliers : 0.00 % Allowed : 15.79 % Favored : 84.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 5.56 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.07 (0.28), residues: 530 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.10 (0.21), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.016 0.008 PHE C 94 HIS 0.003 0.001 HIS C 50 Details of bonding type rmsd covalent geometry : bond 0.01388 ( 3962) covalent geometry : angle 1.60324 ( 5362) hydrogen bonds : bond 0.19117 ( 33) hydrogen bonds : angle 8.64598 ( 99) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.166 Fit side-chains REVERT: B 58 LYS cc_start: 0.3846 (mmtp) cc_final: 0.2863 (pmtt) REVERT: F 59 THR cc_start: 0.5022 (m) cc_final: 0.4651 (t) REVERT: J 50 HIS cc_start: 0.0994 (t-90) cc_final: 0.0688 (t70) outliers start: 0 outliers final: 0 residues processed: 45 average time/residue: 0.5514 time to fit residues: 25.7683 Evaluate side-chains 23 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 23 time to evaluate : 0.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 24 optimal weight: 5.9990 chunk 48 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 16 optimal weight: 8.9990 chunk 32 optimal weight: 0.9990 chunk 31 optimal weight: 5.9990 chunk 25 optimal weight: 10.0000 chunk 19 optimal weight: 0.9990 chunk 30 optimal weight: 10.0000 chunk 22 optimal weight: 0.9980 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 62 GLN ** H 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5409 r_free = 0.5409 target = 0.287231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4967 r_free = 0.4967 target = 0.246468 restraints weight = 4149.161| |-----------------------------------------------------------------------------| r_work (start): 0.4997 rms_B_bonded: 2.74 r_work: 0.4855 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.4855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6300 moved from start: 0.7746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 3962 Z= 0.188 Angle : 0.892 7.848 5362 Z= 0.450 Chirality : 0.056 0.164 670 Planarity : 0.004 0.022 676 Dihedral : 14.498 89.110 596 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 14.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 4.74 % Allowed : 18.16 % Favored : 77.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 5.56 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.52 (0.30), residues: 530 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.67 (0.23), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.021 0.005 PHE F 94 HIS 0.005 0.002 HIS J 50 Details of bonding type rmsd covalent geometry : bond 0.00388 ( 3962) covalent geometry : angle 0.89238 ( 5362) hydrogen bonds : bond 0.02512 ( 33) hydrogen bonds : angle 6.60374 ( 99) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 69 time to evaluate : 0.153 Fit side-chains REVERT: C 99 GLN cc_start: 0.5461 (tm-30) cc_final: 0.4865 (mt0) REVERT: D 88 ILE cc_start: 0.7771 (OUTLIER) cc_final: 0.7552 (mt) REVERT: D 97 LYS cc_start: 0.7625 (ttmm) cc_final: 0.7131 (mttt) REVERT: F 61 GLU cc_start: 0.7589 (OUTLIER) cc_final: 0.7080 (pm20) REVERT: G 99 GLN cc_start: 0.5786 (mt0) cc_final: 0.4844 (mp-120) outliers start: 18 outliers final: 3 residues processed: 80 average time/residue: 0.5050 time to fit residues: 41.8669 Evaluate side-chains 51 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 46 time to evaluate : 0.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 88 ILE Chi-restraints excluded: chain F residue 61 GLU Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain I residue 72 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 7 optimal weight: 10.0000 chunk 43 optimal weight: 6.9990 chunk 10 optimal weight: 20.0000 chunk 28 optimal weight: 1.9990 chunk 29 optimal weight: 20.0000 chunk 16 optimal weight: 0.9980 chunk 44 optimal weight: 0.0070 chunk 45 optimal weight: 7.9990 chunk 36 optimal weight: 6.9990 chunk 1 optimal weight: 9.9990 chunk 35 optimal weight: 20.0000 overall best weight: 3.4004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 65 ASN ** B 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 65 ASN G 62 GLN H 65 ASN I 65 ASN ** J 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4822 r_free = 0.4822 target = 0.195873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.144688 restraints weight = 4146.670| |-----------------------------------------------------------------------------| r_work (start): 0.4179 rms_B_bonded: 2.92 r_work: 0.4030 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.4030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 1.2247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 3962 Z= 0.229 Angle : 0.843 6.146 5362 Z= 0.446 Chirality : 0.056 0.162 670 Planarity : 0.004 0.019 676 Dihedral : 12.822 80.490 596 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 7.37 % Allowed : 19.47 % Favored : 73.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 5.56 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.44 (0.28), residues: 530 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.61 (0.21), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.017 0.003 PHE B 94 HIS 0.003 0.001 HIS F 50 Details of bonding type rmsd covalent geometry : bond 0.00514 ( 3962) covalent geometry : angle 0.84313 ( 5362) hydrogen bonds : bond 0.02768 ( 33) hydrogen bonds : angle 6.17240 ( 99) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 88 time to evaluate : 0.165 Fit side-chains REVERT: A 58 LYS cc_start: 0.6991 (mmtp) cc_final: 0.6574 (mmmt) REVERT: A 80 LYS cc_start: 0.5439 (OUTLIER) cc_final: 0.4408 (tppp) REVERT: B 55 VAL cc_start: 0.8137 (t) cc_final: 0.7868 (p) REVERT: C 60 LYS cc_start: 0.7515 (ttmt) cc_final: 0.6642 (mmtm) REVERT: C 99 GLN cc_start: 0.5647 (tm-30) cc_final: 0.5040 (mt0) REVERT: D 96 LYS cc_start: 0.8395 (ttpt) cc_final: 0.8023 (ttpp) REVERT: E 58 LYS cc_start: 0.6757 (mmtp) cc_final: 0.6061 (mmpt) REVERT: F 60 LYS cc_start: 0.7224 (ttmt) cc_final: 0.6721 (ttmt) REVERT: G 57 GLU cc_start: 0.6628 (OUTLIER) cc_final: 0.6257 (pp20) REVERT: H 60 LYS cc_start: 0.7462 (ttmt) cc_final: 0.6858 (ttmt) REVERT: I 58 LYS cc_start: 0.6846 (mmtp) cc_final: 0.6059 (mmpt) REVERT: I 60 LYS cc_start: 0.7787 (ttmt) cc_final: 0.7059 (mptm) REVERT: I 96 LYS cc_start: 0.7959 (tptp) cc_final: 0.7510 (tptp) REVERT: J 49 VAL cc_start: 0.6614 (OUTLIER) cc_final: 0.6349 (p) outliers start: 28 outliers final: 8 residues processed: 103 average time/residue: 0.6259 time to fit residues: 66.1917 Evaluate side-chains 75 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 64 time to evaluate : 0.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 80 LYS Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain C residue 83 GLU Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain G residue 57 GLU Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 96 LYS Chi-restraints excluded: chain J residue 49 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 39 optimal weight: 8.9990 chunk 8 optimal weight: 0.0020 chunk 37 optimal weight: 5.9990 chunk 45 optimal weight: 20.0000 chunk 44 optimal weight: 20.0000 chunk 24 optimal weight: 9.9990 chunk 23 optimal weight: 2.9990 chunk 46 optimal weight: 7.9990 chunk 33 optimal weight: 1.9990 chunk 34 optimal weight: 9.9990 chunk 12 optimal weight: 0.9990 overall best weight: 2.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 62 GLN D 79 GLN F 99 GLN G 62 GLN H 99 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4712 r_free = 0.4712 target = 0.183731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.131504 restraints weight = 4052.539| |-----------------------------------------------------------------------------| r_work (start): 0.4028 rms_B_bonded: 2.78 r_work: 0.3889 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 1.2816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 3962 Z= 0.141 Angle : 0.632 4.740 5362 Z= 0.329 Chirality : 0.051 0.154 670 Planarity : 0.002 0.014 676 Dihedral : 11.664 85.929 596 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 7.89 % Allowed : 20.00 % Favored : 72.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 5.56 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.26 (0.30), residues: 530 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.48 (0.23), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.011 0.003 PHE J 94 HIS 0.002 0.001 HIS C 50 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 3962) covalent geometry : angle 0.63203 ( 5362) hydrogen bonds : bond 0.01424 ( 33) hydrogen bonds : angle 5.64076 ( 99) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 75 time to evaluate : 0.152 Fit side-chains REVERT: A 60 LYS cc_start: 0.6631 (OUTLIER) cc_final: 0.5987 (ttmt) REVERT: B 79 GLN cc_start: 0.8798 (OUTLIER) cc_final: 0.8547 (mt0) REVERT: C 60 LYS cc_start: 0.7595 (ttmt) cc_final: 0.6608 (mptm) REVERT: C 99 GLN cc_start: 0.5402 (tm-30) cc_final: 0.4897 (mm110) REVERT: D 60 LYS cc_start: 0.6978 (ttmt) cc_final: 0.6382 (mmtm) REVERT: D 96 LYS cc_start: 0.8375 (ttpt) cc_final: 0.8101 (ttpp) REVERT: E 58 LYS cc_start: 0.6535 (mmtp) cc_final: 0.5953 (mmpt) REVERT: E 60 LYS cc_start: 0.6826 (OUTLIER) cc_final: 0.6560 (ttmt) REVERT: F 58 LYS cc_start: 0.6526 (mmtp) cc_final: 0.6162 (mtpt) REVERT: F 60 LYS cc_start: 0.7305 (ttmt) cc_final: 0.7035 (ttmt) REVERT: G 60 LYS cc_start: 0.7196 (ttmt) cc_final: 0.6465 (mptm) REVERT: H 57 GLU cc_start: 0.7042 (pp20) cc_final: 0.6799 (pp20) REVERT: I 58 LYS cc_start: 0.6876 (mmtp) cc_final: 0.6089 (mmpt) REVERT: I 60 LYS cc_start: 0.7874 (ttmt) cc_final: 0.7230 (mptm) REVERT: I 81 THR cc_start: 0.8947 (OUTLIER) cc_final: 0.8693 (p) outliers start: 30 outliers final: 14 residues processed: 96 average time/residue: 0.6645 time to fit residues: 65.4914 Evaluate side-chains 83 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 65 time to evaluate : 0.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 60 LYS Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 79 GLN Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 83 GLU Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 60 LYS Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain I residue 81 THR Chi-restraints excluded: chain J residue 72 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 22 optimal weight: 9.9990 chunk 4 optimal weight: 9.9990 chunk 1 optimal weight: 6.9990 chunk 16 optimal weight: 0.0030 chunk 44 optimal weight: 9.9990 chunk 14 optimal weight: 4.9990 chunk 20 optimal weight: 10.0000 chunk 5 optimal weight: 5.9990 chunk 9 optimal weight: 9.9990 chunk 42 optimal weight: 1.9990 chunk 32 optimal weight: 10.0000 overall best weight: 3.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 GLN A 79 GLN B 62 GLN E 79 GLN F 99 GLN G 79 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4562 r_free = 0.4562 target = 0.172507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.119721 restraints weight = 4115.352| |-----------------------------------------------------------------------------| r_work (start): 0.3864 rms_B_bonded: 2.77 r_work: 0.3730 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work: 0.3593 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 1.3583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.024 3962 Z= 0.203 Angle : 0.718 5.169 5362 Z= 0.376 Chirality : 0.054 0.172 670 Planarity : 0.003 0.018 676 Dihedral : 11.968 89.769 596 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 8.68 % Allowed : 19.21 % Favored : 72.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 5.56 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.37 (0.29), residues: 530 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.56 (0.22), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.011 0.003 PHE E 94 HIS 0.003 0.001 HIS H 50 Details of bonding type rmsd covalent geometry : bond 0.00454 ( 3962) covalent geometry : angle 0.71759 ( 5362) hydrogen bonds : bond 0.01679 ( 33) hydrogen bonds : angle 5.88681 ( 99) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 65 time to evaluate : 0.121 Fit side-chains REVERT: A 58 LYS cc_start: 0.7070 (mmtp) cc_final: 0.6490 (mmmt) REVERT: A 60 LYS cc_start: 0.6698 (OUTLIER) cc_final: 0.6104 (ttmt) REVERT: A 99 GLN cc_start: 0.5726 (mm-40) cc_final: 0.5465 (mm-40) REVERT: B 79 GLN cc_start: 0.8908 (OUTLIER) cc_final: 0.8344 (mt0) REVERT: B 99 GLN cc_start: 0.6294 (mm-40) cc_final: 0.5097 (mm-40) REVERT: C 60 LYS cc_start: 0.7768 (ttmt) cc_final: 0.6697 (mptm) REVERT: C 99 GLN cc_start: 0.5396 (tm-30) cc_final: 0.4686 (mm110) REVERT: D 60 LYS cc_start: 0.7452 (ttmt) cc_final: 0.6618 (mmtm) REVERT: D 96 LYS cc_start: 0.8598 (ttpt) cc_final: 0.8343 (ttpp) REVERT: E 58 LYS cc_start: 0.6541 (mmtp) cc_final: 0.5914 (mmpt) REVERT: E 60 LYS cc_start: 0.6859 (OUTLIER) cc_final: 0.6602 (ttmt) REVERT: F 58 LYS cc_start: 0.7053 (mmtp) cc_final: 0.6335 (mmpt) REVERT: F 60 LYS cc_start: 0.7594 (ttmt) cc_final: 0.7082 (ttmt) REVERT: G 60 LYS cc_start: 0.7562 (ttmt) cc_final: 0.6607 (mptm) REVERT: H 60 LYS cc_start: 0.7740 (ttmt) cc_final: 0.6946 (ttmt) REVERT: I 58 LYS cc_start: 0.7071 (mmtp) cc_final: 0.6348 (mmpt) REVERT: I 60 LYS cc_start: 0.8066 (ttmt) cc_final: 0.7456 (ttmt) REVERT: I 81 THR cc_start: 0.8910 (OUTLIER) cc_final: 0.8656 (p) REVERT: I 96 LYS cc_start: 0.8172 (OUTLIER) cc_final: 0.7937 (tttm) REVERT: J 58 LYS cc_start: 0.6892 (mmtp) cc_final: 0.6131 (mmpt) outliers start: 33 outliers final: 22 residues processed: 86 average time/residue: 0.5531 time to fit residues: 49.0302 Evaluate side-chains 88 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 61 time to evaluate : 0.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 60 LYS Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 79 GLN Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 60 LYS Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 61 GLU Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain I residue 75 THR Chi-restraints excluded: chain I residue 81 THR Chi-restraints excluded: chain I residue 96 LYS Chi-restraints excluded: chain J residue 75 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 40 optimal weight: 20.0000 chunk 18 optimal weight: 6.9990 chunk 12 optimal weight: 8.9990 chunk 17 optimal weight: 1.9990 chunk 8 optimal weight: 8.9990 chunk 46 optimal weight: 20.0000 chunk 22 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 34 optimal weight: 9.9990 chunk 14 optimal weight: 5.9990 chunk 36 optimal weight: 5.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 62 GLN F 99 GLN H 99 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4549 r_free = 0.4549 target = 0.171919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.118312 restraints weight = 4112.798| |-----------------------------------------------------------------------------| r_work (start): 0.3838 rms_B_bonded: 2.81 r_work: 0.3694 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 1.3922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 3962 Z= 0.199 Angle : 0.706 4.984 5362 Z= 0.371 Chirality : 0.053 0.160 670 Planarity : 0.003 0.014 676 Dihedral : 12.019 89.167 596 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 7.63 % Allowed : 20.00 % Favored : 72.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 5.56 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.33 (0.30), residues: 530 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.53 (0.23), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.012 0.003 PHE J 94 HIS 0.005 0.001 HIS D 50 Details of bonding type rmsd covalent geometry : bond 0.00446 ( 3962) covalent geometry : angle 0.70576 ( 5362) hydrogen bonds : bond 0.01528 ( 33) hydrogen bonds : angle 5.81640 ( 99) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 66 time to evaluate : 0.160 Fit side-chains REVERT: A 60 LYS cc_start: 0.6615 (OUTLIER) cc_final: 0.6146 (ttmt) REVERT: A 99 GLN cc_start: 0.5830 (mm-40) cc_final: 0.5570 (mm-40) REVERT: B 79 GLN cc_start: 0.8961 (OUTLIER) cc_final: 0.8454 (mt0) REVERT: B 99 GLN cc_start: 0.6445 (mm-40) cc_final: 0.5244 (mm-40) REVERT: C 60 LYS cc_start: 0.7690 (ttmt) cc_final: 0.6791 (ttmt) REVERT: D 60 LYS cc_start: 0.7548 (ttmt) cc_final: 0.6667 (mmtm) REVERT: D 96 LYS cc_start: 0.8507 (ttpt) cc_final: 0.8281 (ttpp) REVERT: E 58 LYS cc_start: 0.6614 (mmtp) cc_final: 0.5942 (mmpt) REVERT: E 60 LYS cc_start: 0.6741 (OUTLIER) cc_final: 0.6481 (ttmt) REVERT: F 58 LYS cc_start: 0.7315 (mmtp) cc_final: 0.6743 (mmmt) REVERT: F 60 LYS cc_start: 0.7530 (ttmt) cc_final: 0.7039 (ttmt) REVERT: G 58 LYS cc_start: 0.6892 (mmtp) cc_final: 0.6155 (mmpt) REVERT: G 60 LYS cc_start: 0.7486 (ttmt) cc_final: 0.6500 (tptm) REVERT: I 58 LYS cc_start: 0.7085 (mmtp) cc_final: 0.6460 (mmpt) REVERT: I 60 LYS cc_start: 0.7960 (ttmt) cc_final: 0.7363 (ttmt) REVERT: I 81 THR cc_start: 0.8939 (OUTLIER) cc_final: 0.8672 (p) REVERT: J 58 LYS cc_start: 0.6959 (mmtp) cc_final: 0.6276 (mmpt) outliers start: 29 outliers final: 21 residues processed: 84 average time/residue: 0.5672 time to fit residues: 49.1212 Evaluate side-chains 83 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 58 time to evaluate : 0.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 60 LYS Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 79 GLN Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 60 LYS Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 61 GLU Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain I residue 75 THR Chi-restraints excluded: chain I residue 81 THR Chi-restraints excluded: chain J residue 52 VAL Chi-restraints excluded: chain J residue 75 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 45 optimal weight: 20.0000 chunk 1 optimal weight: 3.9990 chunk 24 optimal weight: 20.0000 chunk 33 optimal weight: 0.0870 chunk 42 optimal weight: 0.6980 chunk 8 optimal weight: 6.9990 chunk 40 optimal weight: 9.9990 chunk 18 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 23 optimal weight: 1.9990 chunk 19 optimal weight: 6.9990 overall best weight: 2.1564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 GLN B 62 GLN E 62 GLN F 99 GLN H 99 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4587 r_free = 0.4587 target = 0.174261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.121822 restraints weight = 3842.516| |-----------------------------------------------------------------------------| r_work (start): 0.3908 rms_B_bonded: 2.62 r_work: 0.3757 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.3605 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 1.3964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 3962 Z= 0.123 Angle : 0.581 4.767 5362 Z= 0.303 Chirality : 0.051 0.153 670 Planarity : 0.002 0.014 676 Dihedral : 11.562 87.868 596 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 6.58 % Allowed : 23.16 % Favored : 70.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 5.56 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.19 (0.31), residues: 530 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.43 (0.23), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.009 0.002 PHE G 94 HIS 0.003 0.001 HIS D 50 Details of bonding type rmsd covalent geometry : bond 0.00268 ( 3962) covalent geometry : angle 0.58130 ( 5362) hydrogen bonds : bond 0.01230 ( 33) hydrogen bonds : angle 5.20838 ( 99) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 65 time to evaluate : 0.159 Fit side-chains REVERT: A 58 LYS cc_start: 0.6905 (mmtp) cc_final: 0.6260 (mmpt) REVERT: A 60 LYS cc_start: 0.6633 (tppt) cc_final: 0.6111 (ttmt) REVERT: A 99 GLN cc_start: 0.5932 (mm-40) cc_final: 0.5453 (mm-40) REVERT: B 79 GLN cc_start: 0.8933 (OUTLIER) cc_final: 0.8627 (mt0) REVERT: B 99 GLN cc_start: 0.6223 (mm-40) cc_final: 0.5032 (mm-40) REVERT: C 60 LYS cc_start: 0.7770 (ttmt) cc_final: 0.6889 (ttmt) REVERT: D 60 LYS cc_start: 0.7606 (ttmt) cc_final: 0.6822 (mmtm) REVERT: D 96 LYS cc_start: 0.8498 (ttpt) cc_final: 0.8271 (ttpp) REVERT: E 58 LYS cc_start: 0.6680 (mmtp) cc_final: 0.6050 (mmpt) REVERT: E 99 GLN cc_start: 0.5325 (tp40) cc_final: 0.5006 (mm-40) REVERT: F 58 LYS cc_start: 0.7261 (mmtp) cc_final: 0.6332 (mmpt) REVERT: F 60 LYS cc_start: 0.7514 (ttmt) cc_final: 0.7085 (ttmt) REVERT: G 58 LYS cc_start: 0.6842 (mmtp) cc_final: 0.6045 (mmpt) REVERT: G 60 LYS cc_start: 0.7555 (ttmt) cc_final: 0.6548 (tptm) REVERT: H 57 GLU cc_start: 0.7240 (pp20) cc_final: 0.6994 (tm-30) REVERT: H 60 LYS cc_start: 0.7711 (ttmt) cc_final: 0.6902 (ttmt) REVERT: I 58 LYS cc_start: 0.7115 (mmtp) cc_final: 0.6424 (mmpt) REVERT: I 60 LYS cc_start: 0.8061 (ttmt) cc_final: 0.7437 (ttmt) REVERT: I 81 THR cc_start: 0.8909 (OUTLIER) cc_final: 0.8656 (p) REVERT: J 58 LYS cc_start: 0.6839 (mmtp) cc_final: 0.6162 (mmpt) outliers start: 25 outliers final: 18 residues processed: 81 average time/residue: 0.6805 time to fit residues: 56.5930 Evaluate side-chains 76 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 56 time to evaluate : 0.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 79 GLN Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain I residue 75 THR Chi-restraints excluded: chain I residue 81 THR Chi-restraints excluded: chain J residue 75 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 1 optimal weight: 9.9990 chunk 47 optimal weight: 9.9990 chunk 24 optimal weight: 20.0000 chunk 20 optimal weight: 10.0000 chunk 39 optimal weight: 10.0000 chunk 16 optimal weight: 4.9990 chunk 26 optimal weight: 9.9990 chunk 46 optimal weight: 0.8980 chunk 0 optimal weight: 9.9990 chunk 18 optimal weight: 4.9990 chunk 41 optimal weight: 0.3980 overall best weight: 4.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 GLN B 62 GLN F 99 GLN G 62 GLN H 99 GLN J 62 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4533 r_free = 0.4533 target = 0.170257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.117164 restraints weight = 3812.977| |-----------------------------------------------------------------------------| r_work (start): 0.3840 rms_B_bonded: 2.65 r_work: 0.3687 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.3538 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 1.4144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.025 3962 Z= 0.211 Angle : 0.713 5.118 5362 Z= 0.374 Chirality : 0.053 0.157 670 Planarity : 0.003 0.014 676 Dihedral : 11.853 84.938 596 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 7.89 % Allowed : 21.32 % Favored : 70.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 5.56 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.25 (0.31), residues: 530 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.47 (0.23), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.012 0.003 PHE E 94 HIS 0.003 0.001 HIS D 50 Details of bonding type rmsd covalent geometry : bond 0.00477 ( 3962) covalent geometry : angle 0.71277 ( 5362) hydrogen bonds : bond 0.01651 ( 33) hydrogen bonds : angle 5.71238 ( 99) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 56 time to evaluate : 0.163 Fit side-chains REVERT: A 58 LYS cc_start: 0.7041 (mmtp) cc_final: 0.6426 (mmpt) REVERT: A 60 LYS cc_start: 0.6693 (tppt) cc_final: 0.6142 (ttmt) REVERT: A 99 GLN cc_start: 0.5924 (mm-40) cc_final: 0.5423 (mm-40) REVERT: B 79 GLN cc_start: 0.8982 (OUTLIER) cc_final: 0.8462 (mt0) REVERT: B 80 LYS cc_start: 0.5696 (OUTLIER) cc_final: 0.4748 (ptpp) REVERT: C 60 LYS cc_start: 0.7794 (ttmt) cc_final: 0.6852 (ttmt) REVERT: D 60 LYS cc_start: 0.7756 (ttmt) cc_final: 0.6941 (mmtm) REVERT: D 75 THR cc_start: 0.9078 (OUTLIER) cc_final: 0.8773 (m) REVERT: D 96 LYS cc_start: 0.8520 (ttpt) cc_final: 0.8309 (ttpp) REVERT: E 58 LYS cc_start: 0.6744 (mmtp) cc_final: 0.6077 (mmpt) REVERT: E 99 GLN cc_start: 0.5419 (tp40) cc_final: 0.5126 (mm-40) REVERT: F 58 LYS cc_start: 0.7353 (mmtp) cc_final: 0.6329 (mmpt) REVERT: F 60 LYS cc_start: 0.7587 (ttmt) cc_final: 0.7072 (ttmt) REVERT: G 58 LYS cc_start: 0.6859 (mmtp) cc_final: 0.6153 (mmpt) REVERT: G 60 LYS cc_start: 0.7625 (ttmt) cc_final: 0.6604 (mptm) REVERT: H 58 LYS cc_start: 0.6674 (mmtp) cc_final: 0.6225 (mtpt) REVERT: I 58 LYS cc_start: 0.7063 (mmtp) cc_final: 0.6402 (mmpt) REVERT: I 60 LYS cc_start: 0.8033 (ttmt) cc_final: 0.7408 (ttmt) REVERT: I 81 THR cc_start: 0.8934 (OUTLIER) cc_final: 0.8681 (p) REVERT: J 58 LYS cc_start: 0.6775 (mmtp) cc_final: 0.6105 (mmpt) outliers start: 30 outliers final: 22 residues processed: 79 average time/residue: 0.6072 time to fit residues: 49.4384 Evaluate side-chains 82 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 56 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 79 GLN Chi-restraints excluded: chain B residue 80 LYS Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 61 GLU Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain I residue 75 THR Chi-restraints excluded: chain I residue 81 THR Chi-restraints excluded: chain J residue 75 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 31 optimal weight: 10.0000 chunk 29 optimal weight: 20.0000 chunk 34 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 15 optimal weight: 5.9990 chunk 43 optimal weight: 0.2980 chunk 42 optimal weight: 5.9990 chunk 41 optimal weight: 1.9990 chunk 21 optimal weight: 8.9990 chunk 3 optimal weight: 4.9990 chunk 38 optimal weight: 0.9980 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 62 GLN F 99 GLN H 99 GLN I 99 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4591 r_free = 0.4591 target = 0.175209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.122526 restraints weight = 3785.170| |-----------------------------------------------------------------------------| r_work (start): 0.3920 rms_B_bonded: 2.59 r_work: 0.3768 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.3617 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 1.4178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 3962 Z= 0.114 Angle : 0.568 4.627 5362 Z= 0.295 Chirality : 0.051 0.152 670 Planarity : 0.002 0.013 676 Dihedral : 11.291 80.591 596 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 6.32 % Allowed : 23.68 % Favored : 70.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 5.56 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.16 (0.31), residues: 530 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.40 (0.24), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.008 0.002 PHE E 94 HIS 0.002 0.000 HIS D 50 Details of bonding type rmsd covalent geometry : bond 0.00247 ( 3962) covalent geometry : angle 0.56788 ( 5362) hydrogen bonds : bond 0.01119 ( 33) hydrogen bonds : angle 4.98912 ( 99) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 57 time to evaluate : 0.092 Fit side-chains REVERT: A 60 LYS cc_start: 0.6717 (tppt) cc_final: 0.6279 (ttmt) REVERT: A 99 GLN cc_start: 0.6083 (mm-40) cc_final: 0.5473 (mm-40) REVERT: B 79 GLN cc_start: 0.8867 (OUTLIER) cc_final: 0.8661 (mt0) REVERT: C 60 LYS cc_start: 0.7844 (ttmt) cc_final: 0.7003 (ttmt) REVERT: D 60 LYS cc_start: 0.7773 (ttmt) cc_final: 0.6982 (mmtm) REVERT: D 96 LYS cc_start: 0.8487 (ttpt) cc_final: 0.8198 (tttm) REVERT: E 99 GLN cc_start: 0.5339 (tp40) cc_final: 0.4976 (mm-40) REVERT: F 58 LYS cc_start: 0.7212 (mmtp) cc_final: 0.6327 (mmpt) REVERT: F 60 LYS cc_start: 0.7506 (ttmt) cc_final: 0.7147 (ttmt) REVERT: G 58 LYS cc_start: 0.6956 (mmtp) cc_final: 0.6216 (mmpt) REVERT: G 60 LYS cc_start: 0.7616 (ttmt) cc_final: 0.6614 (tptm) REVERT: H 60 LYS cc_start: 0.7763 (ttmt) cc_final: 0.7001 (ttmt) REVERT: I 58 LYS cc_start: 0.7132 (mmtp) cc_final: 0.6402 (mmpt) REVERT: I 60 LYS cc_start: 0.8053 (ttmt) cc_final: 0.7445 (ttmt) REVERT: I 81 THR cc_start: 0.8945 (OUTLIER) cc_final: 0.8703 (p) REVERT: J 58 LYS cc_start: 0.6792 (mmtp) cc_final: 0.6191 (mmpt) outliers start: 24 outliers final: 20 residues processed: 75 average time/residue: 0.6270 time to fit residues: 48.3761 Evaluate side-chains 77 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 55 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 79 GLN Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 83 GLU Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain I residue 75 THR Chi-restraints excluded: chain I residue 81 THR Chi-restraints excluded: chain J residue 75 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 15 optimal weight: 0.0070 chunk 37 optimal weight: 10.0000 chunk 38 optimal weight: 3.9990 chunk 21 optimal weight: 9.9990 chunk 1 optimal weight: 7.9990 chunk 46 optimal weight: 4.9990 chunk 40 optimal weight: 20.0000 chunk 30 optimal weight: 20.0000 chunk 2 optimal weight: 10.0000 chunk 13 optimal weight: 9.9990 chunk 4 optimal weight: 8.9990 overall best weight: 5.2006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 62 GLN ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 99 GLN H 99 GLN I 99 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4519 r_free = 0.4519 target = 0.169258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.116049 restraints weight = 3822.934| |-----------------------------------------------------------------------------| r_work (start): 0.3822 rms_B_bonded: 2.66 r_work: 0.3677 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3530 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 1.4315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.036 3962 Z= 0.248 Angle : 0.768 5.295 5362 Z= 0.402 Chirality : 0.055 0.158 670 Planarity : 0.003 0.015 676 Dihedral : 11.857 86.336 596 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.17 % Favored : 92.83 % Rotamer: Outliers : 7.37 % Allowed : 21.58 % Favored : 71.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 5.56 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.28 (0.31), residues: 530 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.50 (0.23), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.014 0.003 PHE G 94 HIS 0.004 0.001 HIS D 50 Details of bonding type rmsd covalent geometry : bond 0.00564 ( 3962) covalent geometry : angle 0.76785 ( 5362) hydrogen bonds : bond 0.01758 ( 33) hydrogen bonds : angle 5.77915 ( 99) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 58 time to evaluate : 0.148 Fit side-chains REVERT: A 58 LYS cc_start: 0.7116 (mmtp) cc_final: 0.6364 (mmpt) REVERT: A 60 LYS cc_start: 0.6693 (tppt) cc_final: 0.6165 (ttmt) REVERT: A 99 GLN cc_start: 0.6124 (mm-40) cc_final: 0.5551 (mm-40) REVERT: B 58 LYS cc_start: 0.7159 (mmtp) cc_final: 0.6528 (mmpt) REVERT: B 79 GLN cc_start: 0.8989 (OUTLIER) cc_final: 0.8510 (mt0) REVERT: B 80 LYS cc_start: 0.5619 (OUTLIER) cc_final: 0.4787 (ptpp) REVERT: C 60 LYS cc_start: 0.7830 (ttmt) cc_final: 0.6873 (ttmt) REVERT: D 60 LYS cc_start: 0.7857 (ttmt) cc_final: 0.7040 (mptm) REVERT: D 75 THR cc_start: 0.9080 (OUTLIER) cc_final: 0.8791 (m) REVERT: D 96 LYS cc_start: 0.8569 (ttpt) cc_final: 0.8354 (ttpp) REVERT: E 58 LYS cc_start: 0.6780 (mmtp) cc_final: 0.6059 (mmpt) REVERT: E 99 GLN cc_start: 0.5602 (tp40) cc_final: 0.5191 (mm-40) REVERT: F 58 LYS cc_start: 0.7268 (mmtp) cc_final: 0.6353 (mmpt) REVERT: F 60 LYS cc_start: 0.7631 (ttmt) cc_final: 0.7036 (ttmt) REVERT: G 58 LYS cc_start: 0.6912 (mmtp) cc_final: 0.6204 (mmpt) REVERT: G 60 LYS cc_start: 0.7619 (ttmt) cc_final: 0.6617 (mptm) REVERT: H 58 LYS cc_start: 0.6602 (mmtp) cc_final: 0.6234 (mtpt) REVERT: I 58 LYS cc_start: 0.7048 (mmtp) cc_final: 0.6451 (mmpt) REVERT: I 60 LYS cc_start: 0.8175 (ttmt) cc_final: 0.7468 (ttmt) REVERT: I 81 THR cc_start: 0.8930 (OUTLIER) cc_final: 0.8677 (p) REVERT: J 58 LYS cc_start: 0.6824 (mmtp) cc_final: 0.6120 (mmpt) outliers start: 28 outliers final: 22 residues processed: 79 average time/residue: 0.6153 time to fit residues: 50.0703 Evaluate side-chains 84 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 58 time to evaluate : 0.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 79 GLN Chi-restraints excluded: chain B residue 80 LYS Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 61 GLU Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain I residue 75 THR Chi-restraints excluded: chain I residue 81 THR Chi-restraints excluded: chain J residue 52 VAL Chi-restraints excluded: chain J residue 75 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 5 optimal weight: 10.0000 chunk 14 optimal weight: 5.9990 chunk 46 optimal weight: 7.9990 chunk 43 optimal weight: 10.0000 chunk 37 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 17 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 47 optimal weight: 5.9990 chunk 8 optimal weight: 2.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 62 GLN F 99 GLN H 99 GLN I 99 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4533 r_free = 0.4533 target = 0.171623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.117966 restraints weight = 4074.733| |-----------------------------------------------------------------------------| r_work (start): 0.3844 rms_B_bonded: 2.68 r_work: 0.3701 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.3566 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 1.4355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 3962 Z= 0.168 Angle : 0.655 5.032 5362 Z= 0.342 Chirality : 0.052 0.159 670 Planarity : 0.002 0.018 676 Dihedral : 11.588 84.270 596 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 6.58 % Allowed : 22.89 % Favored : 70.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 5.56 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.27 (0.31), residues: 530 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.48 (0.24), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.011 0.003 PHE G 94 HIS 0.002 0.001 HIS D 50 Details of bonding type rmsd covalent geometry : bond 0.00376 ( 3962) covalent geometry : angle 0.65536 ( 5362) hydrogen bonds : bond 0.01435 ( 33) hydrogen bonds : angle 5.40113 ( 99) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1728.38 seconds wall clock time: 30 minutes 19.64 seconds (1819.64 seconds total)