Starting phenix.real_space_refine on Wed Mar 5 22:26:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x7q_38107/03_2025/8x7q_38107.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x7q_38107/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8x7q_38107/03_2025/8x7q_38107.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x7q_38107/03_2025/8x7q_38107.map" model { file = "/net/cci-nas-00/data/ceres_data/8x7q_38107/03_2025/8x7q_38107.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x7q_38107/03_2025/8x7q_38107.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 2.90, per 1000 atoms: 0.74 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: 0.95 Conformation dependent library (CDL) restraints added in 523.8 milliseconds 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: 0.55 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: 0.87 Time building geometry restraints manager: 1.13 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'F' selection = chain 'I' selection = chain 'H' 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: 1.110 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: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.880 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 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:13.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.710 ------------------------------------------------------------------------------- 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= 0.923 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 HIS 0.003 0.001 HIS C 50 PHE 0.016 0.008 PHE C 94 *********************** 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 : 0.361 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: 1.1078 time to fit residues: 51.8519 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 : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 42 optimal weight: 4.9990 chunk 37 optimal weight: 0.9990 chunk 21 optimal weight: 7.9990 chunk 12 optimal weight: 5.9990 chunk 25 optimal weight: 10.0000 chunk 20 optimal weight: 3.9990 chunk 39 optimal weight: 9.9990 chunk 15 optimal weight: 0.9990 chunk 23 optimal weight: 10.0000 chunk 29 optimal weight: 20.0000 chunk 45 optimal weight: 5.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5033 r_free = 0.5033 target = 0.226114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4509 r_free = 0.4509 target = 0.181337 restraints weight = 3976.312| |-----------------------------------------------------------------------------| r_work (start): 0.4532 rms_B_bonded: 2.87 r_work: 0.4373 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.4373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7312 moved from start: 1.1192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.065 3962 Z= 0.450 Angle : 1.055 7.556 5362 Z= 0.552 Chirality : 0.059 0.182 670 Planarity : 0.005 0.017 676 Dihedral : 14.278 82.193 596 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 17.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 6.58 % Allowed : 17.63 % Favored : 75.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 5.56 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.88 (0.27), residues: 530 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.95 (0.21), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.003 HIS E 50 PHE 0.026 0.005 PHE F 94 *********************** 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 113 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 88 time to evaluate : 0.424 Fit side-chains revert: symmetry clash REVERT: A 49 VAL cc_start: 0.5072 (OUTLIER) cc_final: 0.4513 (p) REVERT: C 99 GLN cc_start: 0.5648 (tm-30) cc_final: 0.5048 (mt0) REVERT: F 49 VAL cc_start: 0.7170 (OUTLIER) cc_final: 0.6505 (p) REVERT: F 60 LYS cc_start: 0.7557 (ttmt) cc_final: 0.6875 (mptm) REVERT: F 61 GLU cc_start: 0.8306 (OUTLIER) cc_final: 0.7852 (pm20) REVERT: F 98 ASP cc_start: 0.7274 (m-30) cc_final: 0.7008 (m-30) REVERT: G 49 VAL cc_start: 0.6677 (OUTLIER) cc_final: 0.6182 (p) REVERT: I 60 LYS cc_start: 0.7653 (ttmt) cc_final: 0.7391 (tppt) outliers start: 25 outliers final: 7 residues processed: 104 average time/residue: 1.1857 time to fit residues: 127.2774 Evaluate side-chains 70 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 59 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 80 LYS Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 61 GLU Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain J residue 52 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 9 optimal weight: 7.9990 chunk 20 optimal weight: 20.0000 chunk 4 optimal weight: 9.9990 chunk 7 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 22 optimal weight: 0.9990 chunk 39 optimal weight: 10.0000 chunk 13 optimal weight: 0.7980 chunk 33 optimal weight: 7.9990 chunk 40 optimal weight: 20.0000 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 GLN C 62 GLN F 99 GLN ** G 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 99 GLN I 65 ASN I 79 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4905 r_free = 0.4905 target = 0.205354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.154892 restraints weight = 3996.415| |-----------------------------------------------------------------------------| r_work (start): 0.4322 rms_B_bonded: 2.87 r_work: 0.4179 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.4179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 1.1723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3962 Z= 0.187 Angle : 0.600 4.536 5362 Z= 0.328 Chirality : 0.052 0.170 670 Planarity : 0.003 0.016 676 Dihedral : 12.724 86.895 596 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 6.05 % Allowed : 25.26 % Favored : 68.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 5.56 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.44 (0.29), residues: 530 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.62 (0.22), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 50 PHE 0.011 0.003 PHE E 94 *********************** 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 95 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 72 time to evaluate : 0.383 Fit side-chains REVERT: C 60 LYS cc_start: 0.7406 (ttmt) cc_final: 0.6670 (mmtp) REVERT: C 99 GLN cc_start: 0.5593 (tm-30) cc_final: 0.5240 (mt0) REVERT: E 79 GLN cc_start: 0.8524 (OUTLIER) cc_final: 0.8255 (mt0) REVERT: F 58 LYS cc_start: 0.5834 (mmtp) cc_final: 0.5342 (mtpt) REVERT: G 57 GLU cc_start: 0.6681 (OUTLIER) cc_final: 0.6451 (pp20) REVERT: H 57 GLU cc_start: 0.6869 (pp20) cc_final: 0.6665 (pp20) REVERT: I 60 LYS cc_start: 0.7850 (ttmt) cc_final: 0.7220 (mptm) REVERT: I 75 THR cc_start: 0.8435 (OUTLIER) cc_final: 0.8190 (m) outliers start: 23 outliers final: 5 residues processed: 83 average time/residue: 1.3016 time to fit residues: 111.1812 Evaluate side-chains 70 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 62 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 79 GLN Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain G residue 57 GLU Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain I residue 75 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 24 optimal weight: 20.0000 chunk 3 optimal weight: 6.9990 chunk 19 optimal weight: 9.9990 chunk 45 optimal weight: 20.0000 chunk 5 optimal weight: 20.0000 chunk 43 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 15 optimal weight: 5.9990 chunk 6 optimal weight: 0.0020 chunk 36 optimal weight: 8.9990 overall best weight: 1.9994 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** C 62 GLN D 79 GLN D 99 GLN E 99 GLN F 99 GLN G 62 GLN G 99 GLN H 79 GLN H 99 GLN J 79 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4705 r_free = 0.4705 target = 0.184835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.131291 restraints weight = 4085.728| |-----------------------------------------------------------------------------| r_work (start): 0.4039 rms_B_bonded: 2.89 r_work: 0.3905 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 1.2870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3962 Z= 0.211 Angle : 0.642 4.677 5362 Z= 0.336 Chirality : 0.051 0.152 670 Planarity : 0.003 0.015 676 Dihedral : 11.898 81.607 596 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 6.84 % Allowed : 25.53 % Favored : 67.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 5.56 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.41 (0.30), residues: 530 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.59 (0.23), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS E 50 PHE 0.012 0.002 PHE E 94 *********************** 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 96 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 70 time to evaluate : 0.378 Fit side-chains REVERT: C 60 LYS cc_start: 0.7489 (ttmt) cc_final: 0.6536 (mmtp) REVERT: C 99 GLN cc_start: 0.5378 (tm-30) cc_final: 0.5140 (mt0) REVERT: D 60 LYS cc_start: 0.6989 (ttmt) cc_final: 0.6311 (mmtp) REVERT: E 58 LYS cc_start: 0.6780 (mmtp) cc_final: 0.6141 (mmpt) REVERT: E 60 LYS cc_start: 0.6725 (tptt) cc_final: 0.6301 (ttmt) REVERT: E 99 GLN cc_start: 0.5185 (tp40) cc_final: 0.4820 (mm-40) REVERT: F 58 LYS cc_start: 0.6628 (mmtp) cc_final: 0.6148 (mtpt) REVERT: F 60 LYS cc_start: 0.7476 (ttmt) cc_final: 0.7000 (ttmt) REVERT: G 60 LYS cc_start: 0.7414 (ttmt) cc_final: 0.6526 (tptm) REVERT: H 60 LYS cc_start: 0.7538 (ttmt) cc_final: 0.6896 (ttmt) REVERT: I 58 LYS cc_start: 0.6941 (mmtp) cc_final: 0.6186 (mmpt) REVERT: I 60 LYS cc_start: 0.7711 (ttmt) cc_final: 0.7418 (ttmt) REVERT: J 58 LYS cc_start: 0.6915 (mmtp) cc_final: 0.6294 (mmpt) outliers start: 26 outliers final: 14 residues processed: 87 average time/residue: 1.2666 time to fit residues: 113.4112 Evaluate side-chains 75 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 61 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain B 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 75 THR Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 96 LYS Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain J residue 52 VAL Chi-restraints excluded: chain J residue 75 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 33 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 40 optimal weight: 20.0000 chunk 46 optimal weight: 10.0000 chunk 34 optimal weight: 5.9990 chunk 42 optimal weight: 4.9990 chunk 2 optimal weight: 10.0000 chunk 38 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 24 optimal weight: 20.0000 chunk 26 optimal weight: 10.0000 overall best weight: 3.1990 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 79 GLN C 62 GLN D 99 GLN E 79 GLN F 99 GLN G 62 GLN H 99 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4595 r_free = 0.4595 target = 0.176108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.123199 restraints weight = 4224.806| |-----------------------------------------------------------------------------| r_work (start): 0.3897 rms_B_bonded: 2.85 r_work: 0.3759 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 1.3433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 3962 Z= 0.272 Angle : 0.663 4.538 5362 Z= 0.347 Chirality : 0.053 0.178 670 Planarity : 0.002 0.013 676 Dihedral : 11.657 81.143 596 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 8.16 % Allowed : 21.84 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.53 (0.29), residues: 530 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.68 (0.22), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 50 PHE 0.009 0.002 PHE F 94 *********************** 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 95 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 64 time to evaluate : 0.418 Fit side-chains REVERT: A 60 LYS cc_start: 0.6491 (OUTLIER) cc_final: 0.5901 (ttmt) REVERT: B 60 LYS cc_start: 0.6753 (tppt) cc_final: 0.6254 (ttmt) REVERT: B 99 GLN cc_start: 0.6132 (mm-40) cc_final: 0.5327 (mm-40) REVERT: C 60 LYS cc_start: 0.7635 (ttmt) cc_final: 0.6622 (mptm) REVERT: D 60 LYS cc_start: 0.7371 (ttmt) cc_final: 0.6593 (mmtm) REVERT: E 58 LYS cc_start: 0.6849 (mmtp) cc_final: 0.6213 (mmpt) REVERT: E 60 LYS cc_start: 0.6705 (OUTLIER) cc_final: 0.6460 (ttmt) REVERT: E 99 GLN cc_start: 0.5438 (tp40) cc_final: 0.4965 (mm-40) REVERT: F 58 LYS cc_start: 0.7109 (mmtp) cc_final: 0.6466 (mtpt) REVERT: F 60 LYS cc_start: 0.7514 (ttmt) cc_final: 0.6941 (ttmt) REVERT: G 49 VAL cc_start: 0.7716 (m) cc_final: 0.7229 (p) REVERT: G 60 LYS cc_start: 0.7466 (ttmt) cc_final: 0.6495 (tptm) REVERT: H 60 LYS cc_start: 0.7579 (ttmt) cc_final: 0.6870 (ttmt) REVERT: H 96 LYS cc_start: 0.8203 (OUTLIER) cc_final: 0.7916 (ttpp) REVERT: I 58 LYS cc_start: 0.7141 (mmtp) cc_final: 0.6416 (mmpt) REVERT: I 60 LYS cc_start: 0.7843 (ttmt) cc_final: 0.7450 (ttmt) REVERT: I 75 THR cc_start: 0.8827 (m) cc_final: 0.8618 (m) REVERT: J 58 LYS cc_start: 0.7027 (mmtp) cc_final: 0.6399 (mmpt) outliers start: 31 outliers final: 19 residues processed: 84 average time/residue: 1.2320 time to fit residues: 106.7064 Evaluate side-chains 83 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 61 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 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 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 75 THR 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 75 THR Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 96 LYS Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain J residue 52 VAL 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 16 optimal weight: 6.9990 chunk 40 optimal weight: 20.0000 chunk 12 optimal weight: 6.9990 chunk 43 optimal weight: 8.9990 chunk 0 optimal weight: 20.0000 chunk 14 optimal weight: 20.0000 chunk 45 optimal weight: 20.0000 chunk 24 optimal weight: 20.0000 chunk 33 optimal weight: 10.0000 chunk 30 optimal weight: 20.0000 chunk 48 optimal weight: 4.9990 overall best weight: 7.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 GLN C 62 GLN C 99 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 = 0.4498 r_free = 0.4498 target = 0.168451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.113910 restraints weight = 3897.161| |-----------------------------------------------------------------------------| r_work (start): 0.3788 rms_B_bonded: 2.72 r_work: 0.3642 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.3492 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 1.4091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.052 3962 Z= 0.561 Angle : 0.943 5.824 5362 Z= 0.495 Chirality : 0.061 0.186 670 Planarity : 0.004 0.015 676 Dihedral : 12.702 72.153 596 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.49 % Favored : 91.51 % Rotamer: Outliers : 9.74 % Allowed : 19.74 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.65 (0.29), residues: 530 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.78 (0.22), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.002 HIS E 50 PHE 0.018 0.004 PHE G 94 *********************** 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 103 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 66 time to evaluate : 0.368 Fit side-chains REVERT: A 60 LYS cc_start: 0.6632 (OUTLIER) cc_final: 0.6040 (ttmt) REVERT: A 99 GLN cc_start: 0.5704 (mm-40) cc_final: 0.5184 (mm-40) REVERT: B 60 LYS cc_start: 0.7043 (tppt) cc_final: 0.6498 (ttmt) REVERT: C 58 LYS cc_start: 0.6784 (mmtp) cc_final: 0.6302 (mmmt) REVERT: C 60 LYS cc_start: 0.7854 (ttmt) cc_final: 0.6775 (mptm) REVERT: D 60 LYS cc_start: 0.7632 (ttmt) cc_final: 0.6883 (mmtm) REVERT: E 58 LYS cc_start: 0.6843 (mmtp) cc_final: 0.6178 (mmpt) REVERT: E 60 LYS cc_start: 0.6829 (OUTLIER) cc_final: 0.6510 (ttmt) REVERT: E 98 ASP cc_start: 0.7839 (m-30) cc_final: 0.7529 (m-30) REVERT: E 99 GLN cc_start: 0.5517 (tp40) cc_final: 0.5077 (mm-40) REVERT: F 58 LYS cc_start: 0.7092 (mmtp) cc_final: 0.6603 (mmmt) REVERT: F 60 LYS cc_start: 0.7587 (ttmt) cc_final: 0.6787 (ttmt) REVERT: G 58 LYS cc_start: 0.6842 (mmtp) cc_final: 0.6120 (mmpt) REVERT: G 60 LYS cc_start: 0.7642 (ttmt) cc_final: 0.6776 (ttmt) REVERT: H 58 LYS cc_start: 0.6644 (mmtp) cc_final: 0.6339 (mtpt) REVERT: H 98 ASP cc_start: 0.8155 (m-30) cc_final: 0.7929 (m-30) REVERT: I 58 LYS cc_start: 0.7098 (mmtp) cc_final: 0.6485 (mmpt) REVERT: I 60 LYS cc_start: 0.8057 (ttmt) cc_final: 0.7403 (ttmt) REVERT: J 58 LYS cc_start: 0.6818 (mmtp) cc_final: 0.6014 (mmpt) outliers start: 37 outliers final: 23 residues processed: 92 average time/residue: 1.0737 time to fit residues: 102.1675 Evaluate side-chains 88 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 63 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 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 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 72 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 57 GLU 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 G residue 96 LYS Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 75 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 4 optimal weight: 0.9980 chunk 25 optimal weight: 20.0000 chunk 8 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 35 optimal weight: 0.9980 chunk 17 optimal weight: 6.9990 chunk 40 optimal weight: 10.0000 chunk 45 optimal weight: 5.9990 chunk 3 optimal weight: 5.9990 chunk 22 optimal weight: 0.9980 chunk 41 optimal weight: 0.0980 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 GLN F 99 GLN H 99 GLN ** I 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4609 r_free = 0.4609 target = 0.176645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.123085 restraints weight = 3765.179| |-----------------------------------------------------------------------------| r_work (start): 0.3929 rms_B_bonded: 2.66 r_work: 0.3796 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3648 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 1.4079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 3962 Z= 0.138 Angle : 0.553 4.435 5362 Z= 0.288 Chirality : 0.051 0.151 670 Planarity : 0.002 0.014 676 Dihedral : 11.568 71.894 596 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 4.21 % Allowed : 24.74 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 HIS 0.002 0.000 HIS D 50 PHE 0.007 0.002 PHE D 94 *********************** 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 75 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 59 time to evaluate : 0.415 Fit side-chains REVERT: A 60 LYS cc_start: 0.6433 (tppt) cc_final: 0.5956 (ttmt) REVERT: B 60 LYS cc_start: 0.6965 (tppt) cc_final: 0.6520 (ttmt) REVERT: B 99 GLN cc_start: 0.6097 (mm-40) cc_final: 0.5684 (mt0) REVERT: C 60 LYS cc_start: 0.7745 (ttmt) cc_final: 0.6890 (ttmt) REVERT: D 60 LYS cc_start: 0.7653 (ttmt) cc_final: 0.6877 (mmtm) REVERT: E 58 LYS cc_start: 0.6679 (mmtp) cc_final: 0.6004 (mmpt) REVERT: E 60 LYS cc_start: 0.6889 (OUTLIER) cc_final: 0.6641 (ttmt) REVERT: E 99 GLN cc_start: 0.5482 (tp40) cc_final: 0.4950 (mm-40) REVERT: F 58 LYS cc_start: 0.7176 (mmtp) cc_final: 0.6553 (mmmt) REVERT: F 60 LYS cc_start: 0.7506 (ttmt) cc_final: 0.6980 (ttmt) REVERT: G 58 LYS cc_start: 0.6954 (mmtp) cc_final: 0.6186 (mmpt) REVERT: G 60 LYS cc_start: 0.7527 (ttmt) cc_final: 0.6678 (ttmt) REVERT: I 58 LYS cc_start: 0.7109 (mmtp) cc_final: 0.6426 (mmpt) REVERT: I 60 LYS cc_start: 0.7791 (ttmt) cc_final: 0.7245 (ttmt) REVERT: J 58 LYS cc_start: 0.6801 (mmtp) cc_final: 0.6092 (mmpt) outliers start: 16 outliers final: 10 residues processed: 71 average time/residue: 1.4540 time to fit residues: 106.1556 Evaluate side-chains 65 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 54 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 60 LYS Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain G residue 75 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 33 optimal weight: 10.0000 chunk 36 optimal weight: 6.9990 chunk 39 optimal weight: 9.9990 chunk 47 optimal weight: 9.9990 chunk 8 optimal weight: 8.9990 chunk 19 optimal weight: 9.9990 chunk 3 optimal weight: 2.9990 chunk 31 optimal weight: 6.9990 chunk 2 optimal weight: 0.9990 chunk 10 optimal weight: 30.0000 chunk 9 optimal weight: 7.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 GLN ** C 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 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 = 0.4517 r_free = 0.4517 target = 0.169634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.115064 restraints weight = 3818.737| |-----------------------------------------------------------------------------| r_work (start): 0.3814 rms_B_bonded: 2.68 r_work: 0.3665 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.3509 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 1.4251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 3962 Z= 0.399 Angle : 0.778 5.306 5362 Z= 0.409 Chirality : 0.056 0.169 670 Planarity : 0.003 0.015 676 Dihedral : 12.331 67.656 596 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.17 % Favored : 92.83 % Rotamer: Outliers : 8.16 % Allowed : 22.11 % Favored : 69.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 5.56 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.60 (0.30), residues: 530 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.73 (0.23), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS E 50 PHE 0.014 0.003 PHE J 94 *********************** 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 92 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 61 time to evaluate : 0.422 Fit side-chains REVERT: A 60 LYS cc_start: 0.6624 (OUTLIER) cc_final: 0.6083 (ttmt) REVERT: A 80 LYS cc_start: 0.8899 (OUTLIER) cc_final: 0.7907 (tmtt) REVERT: B 58 LYS cc_start: 0.7109 (mmtp) cc_final: 0.6478 (mmpt) REVERT: B 60 LYS cc_start: 0.6954 (tppt) cc_final: 0.6421 (ttmt) REVERT: C 58 LYS cc_start: 0.6773 (mmtp) cc_final: 0.6445 (mmmt) REVERT: C 60 LYS cc_start: 0.7758 (ttmt) cc_final: 0.6813 (ttmt) REVERT: D 60 LYS cc_start: 0.7808 (ttmt) cc_final: 0.6977 (mmtm) REVERT: E 58 LYS cc_start: 0.6759 (mmtp) cc_final: 0.6128 (mmpt) REVERT: E 60 LYS cc_start: 0.6670 (OUTLIER) cc_final: 0.6454 (ttmt) REVERT: F 58 LYS cc_start: 0.7217 (mmtp) cc_final: 0.6571 (mmmt) REVERT: F 60 LYS cc_start: 0.7517 (ttmt) cc_final: 0.6895 (ttmt) REVERT: G 58 LYS cc_start: 0.6902 (mmtp) cc_final: 0.6193 (mmpt) REVERT: G 60 LYS cc_start: 0.7649 (ttmt) cc_final: 0.6773 (ttmt) REVERT: H 57 GLU cc_start: 0.7343 (pp20) cc_final: 0.7124 (tm-30) REVERT: H 58 LYS cc_start: 0.6544 (mmtp) cc_final: 0.6219 (mtpt) REVERT: I 58 LYS cc_start: 0.7120 (mmtp) cc_final: 0.6505 (mmpt) REVERT: I 60 LYS cc_start: 0.8096 (ttmt) cc_final: 0.7433 (ttmt) REVERT: J 58 LYS cc_start: 0.6753 (mmtp) cc_final: 0.6084 (mmpt) outliers start: 31 outliers final: 22 residues processed: 80 average time/residue: 1.2021 time to fit residues: 99.2547 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 : 0.377 ------------------------------------------------------------------------------- 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 A residue 80 LYS Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 75 THR 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 E residue 52 VAL Chi-restraints excluded: chain E residue 60 LYS Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 96 LYS 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 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 J residue 75 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 8 optimal weight: 9.9990 chunk 22 optimal weight: 6.9990 chunk 43 optimal weight: 0.9990 chunk 27 optimal weight: 6.9990 chunk 9 optimal weight: 9.9990 chunk 2 optimal weight: 0.9980 chunk 15 optimal weight: 0.7980 chunk 25 optimal weight: 20.0000 chunk 10 optimal weight: 20.0000 chunk 20 optimal weight: 7.9990 chunk 34 optimal weight: 10.0000 overall best weight: 3.3586 ------------------------------------------------------------------------------- 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** ** C 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 99 GLN H 99 GLN I 62 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4548 r_free = 0.4548 target = 0.171529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.117364 restraints weight = 3826.190| |-----------------------------------------------------------------------------| r_work (start): 0.3851 rms_B_bonded: 2.67 r_work: 0.3705 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.3551 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 1.4305 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= 0.268 Angle : 0.658 5.073 5362 Z= 0.344 Chirality : 0.053 0.158 670 Planarity : 0.002 0.014 676 Dihedral : 12.059 66.845 596 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 6.05 % Allowed : 24.21 % Favored : 69.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 5.56 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.51 (0.31), 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 HIS 0.002 0.001 HIS D 50 PHE 0.012 0.003 PHE G 94 *********************** 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: 23 poor density : 58 time to evaluate : 0.362 Fit side-chains REVERT: A 60 LYS cc_start: 0.6499 (tppt) cc_final: 0.6009 (ttmt) REVERT: A 80 LYS cc_start: 0.8872 (OUTLIER) cc_final: 0.7899 (tmtt) REVERT: B 60 LYS cc_start: 0.6898 (tppt) cc_final: 0.6433 (ttmt) REVERT: C 60 LYS cc_start: 0.7770 (ttmt) cc_final: 0.6903 (ttmt) REVERT: D 60 LYS cc_start: 0.7832 (ttmt) cc_final: 0.6983 (mmtm) REVERT: E 58 LYS cc_start: 0.6669 (mmtp) cc_final: 0.6034 (mmpt) REVERT: F 58 LYS cc_start: 0.7186 (mmtp) cc_final: 0.6281 (mmpt) REVERT: F 60 LYS cc_start: 0.7469 (ttmt) cc_final: 0.6916 (ttmt) REVERT: G 58 LYS cc_start: 0.6955 (mmtp) cc_final: 0.6253 (mmpt) REVERT: G 60 LYS cc_start: 0.7611 (ttmt) cc_final: 0.6720 (ttmt) REVERT: I 58 LYS cc_start: 0.7195 (mmtp) cc_final: 0.6601 (mmpt) REVERT: I 60 LYS cc_start: 0.7933 (ttmt) cc_final: 0.7354 (ttmt) REVERT: J 58 LYS cc_start: 0.6731 (mmtp) cc_final: 0.6090 (mmpt) outliers start: 23 outliers final: 19 residues processed: 76 average time/residue: 1.2019 time to fit residues: 94.2155 Evaluate side-chains 74 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 54 time to evaluate : 0.420 ------------------------------------------------------------------------------- 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 A residue 80 LYS Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 62 GLN Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain E residue 72 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 66 VAL Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain I 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 14 optimal weight: 8.9990 chunk 45 optimal weight: 30.0000 chunk 26 optimal weight: 3.9990 chunk 49 optimal weight: 9.9990 chunk 29 optimal weight: 20.0000 chunk 21 optimal weight: 10.0000 chunk 37 optimal weight: 10.0000 chunk 44 optimal weight: 2.9990 chunk 2 optimal weight: 8.9990 chunk 11 optimal weight: 10.0000 chunk 34 optimal weight: 5.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- 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** ** C 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 99 GLN H 99 GLN I 62 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4479 r_free = 0.4479 target = 0.168355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.113588 restraints weight = 4086.052| |-----------------------------------------------------------------------------| r_work (start): 0.3780 rms_B_bonded: 2.74 r_work: 0.3646 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.3510 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 1.4458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.044 3962 Z= 0.456 Angle : 0.822 5.549 5362 Z= 0.433 Chirality : 0.057 0.169 670 Planarity : 0.003 0.014 676 Dihedral : 12.913 69.213 596 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.43 % Favored : 90.57 % Rotamer: Outliers : 7.63 % Allowed : 22.89 % Favored : 69.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 5.56 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.58 (0.31), residues: 530 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.72 (0.23), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS E 50 PHE 0.016 0.004 PHE G 94 ********************** 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 93 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 64 time to evaluate : 0.404 Fit side-chains REVERT: A 60 LYS cc_start: 0.6749 (OUTLIER) cc_final: 0.6269 (ttmt) REVERT: A 80 LYS cc_start: 0.8888 (OUTLIER) cc_final: 0.7893 (tmtt) REVERT: B 58 LYS cc_start: 0.7059 (mmtp) cc_final: 0.6451 (mmmt) REVERT: B 60 LYS cc_start: 0.7047 (tppt) cc_final: 0.6463 (ttmt) REVERT: C 58 LYS cc_start: 0.7089 (mmtp) cc_final: 0.6683 (mmmt) REVERT: C 60 LYS cc_start: 0.7884 (ttmt) cc_final: 0.6939 (ttmt) REVERT: D 60 LYS cc_start: 0.7890 (ttmt) cc_final: 0.7092 (mptm) REVERT: E 58 LYS cc_start: 0.6789 (mmtp) cc_final: 0.6195 (mmpt) REVERT: E 98 ASP cc_start: 0.7965 (m-30) cc_final: 0.7647 (m-30) REVERT: F 58 LYS cc_start: 0.7252 (mmtp) cc_final: 0.6603 (mmmt) REVERT: F 60 LYS cc_start: 0.7641 (ttmt) cc_final: 0.6975 (ttmt) REVERT: G 58 LYS cc_start: 0.6942 (mmtp) cc_final: 0.6254 (mmpt) REVERT: G 60 LYS cc_start: 0.7721 (ttmt) cc_final: 0.6852 (ttmt) REVERT: H 57 GLU cc_start: 0.7321 (pp20) cc_final: 0.7065 (tm-30) REVERT: H 58 LYS cc_start: 0.6673 (mmtp) cc_final: 0.6345 (mtpt) REVERT: I 58 LYS cc_start: 0.7160 (mmtp) cc_final: 0.6559 (mmpt) REVERT: I 60 LYS cc_start: 0.8097 (ttmt) cc_final: 0.7448 (ttmt) REVERT: J 58 LYS cc_start: 0.6716 (mmtp) cc_final: 0.6051 (mmpt) outliers start: 29 outliers final: 27 residues processed: 83 average time/residue: 1.2444 time to fit residues: 106.6708 Evaluate side-chains 89 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 60 time to evaluate : 0.421 ------------------------------------------------------------------------------- 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 A residue 80 LYS Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 62 GLN Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 59 THR 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 72 THR Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 96 LYS 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 52 VAL 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 2 optimal weight: 8.9990 chunk 22 optimal weight: 2.9990 chunk 7 optimal weight: 0.0980 chunk 0 optimal weight: 20.0000 chunk 5 optimal weight: 20.0000 chunk 28 optimal weight: 0.9980 chunk 8 optimal weight: 5.9990 chunk 44 optimal weight: 9.9990 chunk 21 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- 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 C 62 GLN ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 99 GLN H 99 GLN I 62 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4605 r_free = 0.4605 target = 0.176020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.121505 restraints weight = 3791.317| |-----------------------------------------------------------------------------| r_work (start): 0.3916 rms_B_bonded: 2.68 r_work: 0.3780 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3632 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 1.4441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 3962 Z= 0.153 Angle : 0.564 4.838 5362 Z= 0.294 Chirality : 0.051 0.147 670 Planarity : 0.002 0.013 676 Dihedral : 11.980 66.405 596 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 4.74 % Allowed : 25.79 % Favored : 69.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 5.56 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.46 (0.31), residues: 530 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.63 (0.24), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS E 50 PHE 0.008 0.002 PHE G 94 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3222.20 seconds wall clock time: 55 minutes 56.56 seconds (3356.56 seconds total)