Starting phenix.real_space_refine on Mon Jan 13 20:08:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x7q_38107/01_2025/8x7q_38107.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x7q_38107/01_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_38107/01_2025/8x7q_38107.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x7q_38107/01_2025/8x7q_38107.map" model { file = "/net/cci-nas-00/data/ceres_data/8x7q_38107/01_2025/8x7q_38107.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x7q_38107/01_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-5571/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: 3.59, per 1000 atoms: 0.91 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: 1.02 Conformation dependent library (CDL) restraints added in 589.5 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: 0.52 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: 0.99 Time building geometry restraints manager: 1.24 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: 1.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 15.260 Find NCS groups from input model: 0.070 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:13.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.450 ------------------------------------------------------------------------------- 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 : 0.420 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: 1.1730 time to fit residues: 54.9008 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 : 0.410 ------------------------------------------------------------------------------- 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 = 0.181339 restraints weight = 3976.315| |-----------------------------------------------------------------------------| r_work (start): 0.4532 rms_B_bonded: 2.87 r_work: 0.4372 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.4372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7313 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 : 0.373 Fit side-chains revert: symmetry clash REVERT: A 49 VAL cc_start: 0.5076 (OUTLIER) cc_final: 0.4516 (p) REVERT: C 99 GLN cc_start: 0.5651 (tm-30) cc_final: 0.5053 (mt0) REVERT: F 49 VAL cc_start: 0.7178 (OUTLIER) cc_final: 0.6515 (p) REVERT: F 60 LYS cc_start: 0.7559 (ttmt) cc_final: 0.6877 (mptm) REVERT: F 61 GLU cc_start: 0.8309 (OUTLIER) cc_final: 0.7855 (pm20) REVERT: F 98 ASP cc_start: 0.7275 (m-30) cc_final: 0.7010 (m-30) REVERT: G 49 VAL cc_start: 0.6687 (OUTLIER) cc_final: 0.6195 (p) REVERT: I 60 LYS cc_start: 0.7651 (ttmt) cc_final: 0.7394 (tppt) outliers start: 25 outliers final: 7 residues processed: 104 average time/residue: 1.1537 time to fit residues: 123.8213 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 : 0.440 ------------------------------------------------------------------------------- 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: 10.0000 chunk 20 optimal weight: 20.0000 chunk 4 optimal weight: 9.9990 chunk 7 optimal weight: 4.9990 chunk 42 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 chunk 39 optimal weight: 10.0000 chunk 13 optimal weight: 0.7980 chunk 33 optimal weight: 4.9990 chunk 40 optimal weight: 20.0000 overall best weight: 2.3186 ------------------------------------------------------------------------------- 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 G 99 GLN I 65 ASN I 79 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4799 r_free = 0.4799 target = 0.193820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.141713 restraints weight = 4004.621| |-----------------------------------------------------------------------------| r_work (start): 0.4160 rms_B_bonded: 2.88 r_work: 0.4011 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.4011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 1.2038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3962 Z= 0.236 Angle : 0.687 4.945 5362 Z= 0.370 Chirality : 0.053 0.167 670 Planarity : 0.003 0.016 676 Dihedral : 12.844 83.588 596 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 8.68 % Allowed : 23.16 % Favored : 68.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 5.56 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -3.49 (0.28), residues: 530 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.66 (0.22), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 50 PHE 0.014 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 111 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 78 time to evaluate : 0.353 Fit side-chains REVERT: A 79 GLN cc_start: 0.9004 (OUTLIER) cc_final: 0.8738 (mt0) REVERT: C 60 LYS cc_start: 0.7400 (ttmt) cc_final: 0.6599 (mmtp) REVERT: C 99 GLN cc_start: 0.5641 (tm-30) cc_final: 0.5096 (mt0) REVERT: E 58 LYS cc_start: 0.6646 (mmtp) cc_final: 0.5957 (mmpt) REVERT: E 60 LYS cc_start: 0.6705 (OUTLIER) cc_final: 0.6184 (ttmt) REVERT: F 58 LYS cc_start: 0.6354 (mmtp) cc_final: 0.6091 (mtpt) REVERT: F 60 LYS cc_start: 0.7275 (ttmt) cc_final: 0.6852 (ttmt) REVERT: G 60 LYS cc_start: 0.7255 (ttmt) cc_final: 0.6572 (mptm) REVERT: H 60 LYS cc_start: 0.7486 (ttmt) cc_final: 0.6842 (ttmt) REVERT: I 58 LYS cc_start: 0.6833 (mmtp) cc_final: 0.6055 (mmpt) REVERT: I 60 LYS cc_start: 0.8000 (ttmt) cc_final: 0.7456 (ttmt) REVERT: J 79 GLN cc_start: 0.8589 (OUTLIER) cc_final: 0.8313 (mt0) outliers start: 33 outliers final: 9 residues processed: 101 average time/residue: 1.3732 time to fit residues: 142.4121 Evaluate side-chains 72 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 60 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 79 GLN Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain C residue 52 VAL 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 75 THR Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain J residue 79 GLN 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: 4.9990 chunk 19 optimal weight: 9.9990 chunk 45 optimal weight: 30.0000 chunk 5 optimal weight: 2.9990 chunk 43 optimal weight: 6.9990 chunk 38 optimal weight: 2.9990 chunk 14 optimal weight: 20.0000 chunk 15 optimal weight: 4.9990 chunk 6 optimal weight: 0.0030 chunk 36 optimal weight: 1.9990 overall best weight: 2.5998 ------------------------------------------------------------------------------- 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 B 79 GLN C 62 GLN C 79 GLN D 79 GLN E 79 GLN F 62 GLN F 99 GLN G 62 GLN G 99 GLN H 99 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4636 r_free = 0.4636 target = 0.178787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.126176 restraints weight = 4104.321| |-----------------------------------------------------------------------------| r_work (start): 0.3956 rms_B_bonded: 2.81 r_work: 0.3819 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 1.3105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3962 Z= 0.230 Angle : 0.655 4.821 5362 Z= 0.342 Chirality : 0.052 0.160 670 Planarity : 0.002 0.014 676 Dihedral : 11.982 80.502 596 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 7.89 % Allowed : 21.58 % 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: -3.51 (0.29), residues: 530 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.67 (0.22), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS E 50 PHE 0.011 0.003 PHE A 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 94 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 64 time to evaluate : 0.355 Fit side-chains REVERT: A 79 GLN cc_start: 0.8793 (OUTLIER) cc_final: 0.8279 (mt0) REVERT: C 60 LYS cc_start: 0.7529 (ttmt) cc_final: 0.6543 (mptm) REVERT: C 99 GLN cc_start: 0.5195 (tm-30) cc_final: 0.4746 (mm110) REVERT: D 60 LYS cc_start: 0.7046 (ttmt) cc_final: 0.6393 (mmtp) REVERT: D 99 GLN cc_start: 0.5768 (tt0) cc_final: 0.5423 (mt0) REVERT: E 58 LYS cc_start: 0.6810 (mmtp) cc_final: 0.6220 (mmpt) REVERT: E 60 LYS cc_start: 0.6830 (OUTLIER) cc_final: 0.6315 (ttmt) REVERT: E 99 GLN cc_start: 0.5627 (tp40) cc_final: 0.5270 (mm-40) REVERT: F 58 LYS cc_start: 0.6900 (mmtp) cc_final: 0.6344 (mtpt) REVERT: F 60 LYS cc_start: 0.7420 (ttmt) cc_final: 0.6900 (ttmt) REVERT: F 79 GLN cc_start: 0.8922 (OUTLIER) cc_final: 0.8706 (tt0) REVERT: G 57 GLU cc_start: 0.7022 (OUTLIER) cc_final: 0.6410 (pp20) REVERT: G 60 LYS cc_start: 0.7488 (ttmt) cc_final: 0.6503 (tptm) REVERT: H 60 LYS cc_start: 0.7478 (ttmt) cc_final: 0.6816 (ttmt) REVERT: H 96 LYS cc_start: 0.8289 (OUTLIER) cc_final: 0.8007 (ttpp) REVERT: I 58 LYS cc_start: 0.7016 (mmtp) cc_final: 0.6300 (mmpt) REVERT: I 60 LYS cc_start: 0.7751 (ttmt) cc_final: 0.7329 (ttmt) REVERT: J 58 LYS cc_start: 0.7062 (mmtp) cc_final: 0.6328 (mmpt) outliers start: 30 outliers final: 15 residues processed: 86 average time/residue: 1.2656 time to fit residues: 112.1355 Evaluate side-chains 78 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 58 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 79 GLN Chi-restraints excluded: chain B residue 52 VAL 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 D residue 81 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 75 THR Chi-restraints excluded: chain F residue 79 GLN Chi-restraints excluded: chain G residue 57 GLU Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 96 LYS 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: 0.7980 chunk 16 optimal weight: 0.8980 chunk 40 optimal weight: 20.0000 chunk 46 optimal weight: 20.0000 chunk 34 optimal weight: 9.9990 chunk 42 optimal weight: 5.9990 chunk 2 optimal weight: 10.0000 chunk 38 optimal weight: 0.3980 chunk 0 optimal weight: 20.0000 chunk 24 optimal weight: 20.0000 chunk 26 optimal weight: 8.9990 overall best weight: 3.4184 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** C 62 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 = 0.4570 r_free = 0.4570 target = 0.174571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.120832 restraints weight = 4171.150| |-----------------------------------------------------------------------------| r_work (start): 0.3869 rms_B_bonded: 2.84 r_work: 0.3737 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 1.3637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 3962 Z= 0.285 Angle : 0.689 4.748 5362 Z= 0.361 Chirality : 0.053 0.155 670 Planarity : 0.002 0.013 676 Dihedral : 11.758 78.017 596 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 8.68 % Allowed : 21.05 % 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 (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: -3.62 (0.29), residues: 530 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.75 (0.22), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 50 PHE 0.011 0.003 PHE G 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 94 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 61 time to evaluate : 0.430 Fit side-chains REVERT: A 60 LYS cc_start: 0.6582 (OUTLIER) cc_final: 0.6158 (ttmt) REVERT: A 99 GLN cc_start: 0.5827 (mm-40) cc_final: 0.5448 (mm-40) REVERT: C 60 LYS cc_start: 0.7600 (ttmt) cc_final: 0.6639 (mptm) REVERT: D 60 LYS cc_start: 0.7358 (ttmt) cc_final: 0.6560 (mmtm) REVERT: E 58 LYS cc_start: 0.6937 (mmtp) cc_final: 0.6334 (mmpt) REVERT: E 60 LYS cc_start: 0.6808 (OUTLIER) cc_final: 0.6260 (ttmt) REVERT: E 99 GLN cc_start: 0.5459 (tp40) cc_final: 0.5105 (mm-40) REVERT: F 58 LYS cc_start: 0.7260 (mmtp) cc_final: 0.6261 (mmpt) REVERT: F 60 LYS cc_start: 0.7564 (ttmt) cc_final: 0.6965 (ttmt) REVERT: G 49 VAL cc_start: 0.7738 (m) cc_final: 0.7273 (p) REVERT: G 58 LYS cc_start: 0.7059 (mmtp) cc_final: 0.6350 (mmpt) REVERT: G 60 LYS cc_start: 0.7666 (ttmt) cc_final: 0.6753 (ttmt) REVERT: H 57 GLU cc_start: 0.7063 (pp20) cc_final: 0.6803 (tm-30) REVERT: H 60 LYS cc_start: 0.7529 (ttmt) cc_final: 0.6818 (ttmt) REVERT: H 96 LYS cc_start: 0.8250 (OUTLIER) cc_final: 0.8033 (ttpp) REVERT: I 58 LYS cc_start: 0.7158 (mmtp) cc_final: 0.6510 (mmpt) REVERT: I 60 LYS cc_start: 0.7931 (ttmt) cc_final: 0.7411 (ttmt) REVERT: J 58 LYS cc_start: 0.6988 (mmtp) cc_final: 0.6384 (mmpt) outliers start: 33 outliers final: 18 residues processed: 83 average time/residue: 1.3105 time to fit residues: 112.0435 Evaluate side-chains 76 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 55 time to evaluate : 0.413 ------------------------------------------------------------------------------- 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 75 THR Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 81 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 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 16 optimal weight: 8.9990 chunk 40 optimal weight: 20.0000 chunk 12 optimal weight: 9.9990 chunk 43 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 14 optimal weight: 3.9990 chunk 45 optimal weight: 10.0000 chunk 24 optimal weight: 20.0000 chunk 33 optimal weight: 0.9990 chunk 30 optimal weight: 20.0000 chunk 48 optimal weight: 5.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 62 GLN C 99 GLN D 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 = 0.4515 r_free = 0.4515 target = 0.168806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.114668 restraints weight = 3894.506| |-----------------------------------------------------------------------------| r_work (start): 0.3803 rms_B_bonded: 2.70 r_work: 0.3667 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3513 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 1.4023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.038 3962 Z= 0.451 Angle : 0.830 5.364 5362 Z= 0.437 Chirality : 0.058 0.173 670 Planarity : 0.003 0.014 676 Dihedral : 12.524 74.860 596 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 8.68 % Allowed : 20.53 % 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 (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: -3.61 (0.29), residues: 530 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.75 (0.22), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS E 50 PHE 0.016 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 93 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 60 time to evaluate : 0.448 Fit side-chains REVERT: A 60 LYS cc_start: 0.6501 (OUTLIER) cc_final: 0.6074 (ttmt) REVERT: A 99 GLN cc_start: 0.5709 (mm-40) cc_final: 0.5344 (mm-40) REVERT: B 58 LYS cc_start: 0.7297 (mmtp) cc_final: 0.6577 (mmpt) REVERT: C 60 LYS cc_start: 0.7752 (ttmt) cc_final: 0.6682 (mptm) REVERT: D 60 LYS cc_start: 0.7639 (ttmt) cc_final: 0.6803 (mmtm) REVERT: E 58 LYS cc_start: 0.6863 (mmtp) cc_final: 0.6174 (mmpt) REVERT: E 60 LYS cc_start: 0.6808 (OUTLIER) cc_final: 0.6285 (ttmt) REVERT: F 58 LYS cc_start: 0.7201 (mmtp) cc_final: 0.6605 (mmmt) REVERT: F 60 LYS cc_start: 0.7580 (ttmt) cc_final: 0.6826 (ttmt) REVERT: G 58 LYS cc_start: 0.6904 (mmtp) cc_final: 0.6489 (mmmt) REVERT: G 60 LYS cc_start: 0.7661 (ttmt) cc_final: 0.6767 (ttmt) REVERT: H 96 LYS cc_start: 0.8425 (OUTLIER) cc_final: 0.8206 (ttpp) REVERT: I 58 LYS cc_start: 0.7107 (mmtp) cc_final: 0.6505 (mmpt) REVERT: I 60 LYS cc_start: 0.8080 (ttmt) cc_final: 0.7397 (ttmt) REVERT: J 58 LYS cc_start: 0.6826 (mmtp) cc_final: 0.6116 (mmpt) REVERT: J 99 GLN cc_start: 0.5875 (mm-40) cc_final: 0.5548 (mm-40) outliers start: 33 outliers final: 24 residues processed: 83 average time/residue: 1.1193 time to fit residues: 96.0933 Evaluate side-chains 84 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 57 time to evaluate : 0.404 ------------------------------------------------------------------------------- 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 D residue 81 THR Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 60 LYS 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 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 H residue 52 VAL Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain H residue 96 LYS Chi-restraints excluded: chain I 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: 3.9990 chunk 25 optimal weight: 20.0000 chunk 8 optimal weight: 7.9990 chunk 28 optimal weight: 5.9990 chunk 35 optimal weight: 5.9990 chunk 17 optimal weight: 8.9990 chunk 40 optimal weight: 20.0000 chunk 45 optimal weight: 5.9990 chunk 3 optimal weight: 5.9990 chunk 22 optimal weight: 5.9990 chunk 41 optimal weight: 0.0970 overall best weight: 4.4186 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** C 62 GLN C 99 GLN 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 = 0.4533 r_free = 0.4533 target = 0.170328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.116405 restraints weight = 3814.071| |-----------------------------------------------------------------------------| r_work (start): 0.3834 rms_B_bonded: 2.68 r_work: 0.3691 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3539 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 1.4168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 3962 Z= 0.337 Angle : 0.717 5.233 5362 Z= 0.376 Chirality : 0.054 0.158 670 Planarity : 0.003 0.014 676 Dihedral : 12.328 80.590 596 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 9.21 % Allowed : 20.00 % 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 (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: -3.55 (0.29), residues: 530 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.70 (0.22), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS D 50 PHE 0.013 0.003 PHE G 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 89 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 54 time to evaluate : 0.409 Fit side-chains REVERT: A 60 LYS cc_start: 0.6606 (OUTLIER) cc_final: 0.6199 (ttmt) REVERT: A 80 LYS cc_start: 0.8889 (OUTLIER) cc_final: 0.7743 (tmtt) REVERT: C 60 LYS cc_start: 0.7815 (ttmt) cc_final: 0.6850 (ttmt) REVERT: D 60 LYS cc_start: 0.7797 (ttmt) cc_final: 0.6916 (mmtm) REVERT: E 58 LYS cc_start: 0.6798 (mmtp) cc_final: 0.6185 (mmpt) REVERT: E 60 LYS cc_start: 0.6743 (OUTLIER) cc_final: 0.6239 (ttmt) REVERT: F 58 LYS cc_start: 0.7136 (mmtp) cc_final: 0.6561 (mmmt) REVERT: F 60 LYS cc_start: 0.7596 (ttmt) cc_final: 0.6907 (ttmt) REVERT: G 58 LYS cc_start: 0.6933 (mmtp) cc_final: 0.6175 (mmpt) REVERT: G 60 LYS cc_start: 0.7623 (ttmt) cc_final: 0.6756 (ttmt) REVERT: I 58 LYS cc_start: 0.7147 (mmtp) cc_final: 0.6558 (mmpt) REVERT: I 60 LYS cc_start: 0.8050 (ttmt) cc_final: 0.7410 (ttmt) REVERT: J 58 LYS cc_start: 0.6822 (mmtp) cc_final: 0.6165 (mmpt) outliers start: 35 outliers final: 25 residues processed: 79 average time/residue: 1.2388 time to fit residues: 101.0863 Evaluate side-chains 79 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 51 time to evaluate : 0.402 ------------------------------------------------------------------------------- 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 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 75 THR Chi-restraints excluded: chain D residue 81 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 57 GLU 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 I residue 75 THR Chi-restraints excluded: chain I residue 96 LYS Chi-restraints excluded: chain J residue 52 VAL 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: 4.9990 chunk 39 optimal weight: 7.9990 chunk 47 optimal weight: 9.9990 chunk 8 optimal weight: 7.9990 chunk 19 optimal weight: 20.0000 chunk 3 optimal weight: 6.9990 chunk 31 optimal weight: 10.0000 chunk 2 optimal weight: 0.9990 chunk 10 optimal weight: 20.0000 chunk 9 optimal weight: 9.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** C 62 GLN ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 99 GLN ** I 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 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 = 0.4482 r_free = 0.4482 target = 0.168038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.113877 restraints weight = 4049.087| |-----------------------------------------------------------------------------| r_work (start): 0.3779 rms_B_bonded: 2.72 r_work: 0.3637 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.3501 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 1.4319 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= 0.433 Angle : 0.809 5.619 5362 Z= 0.425 Chirality : 0.057 0.174 670 Planarity : 0.003 0.015 676 Dihedral : 12.824 83.355 596 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.17 % Favored : 92.83 % Rotamer: Outliers : 9.21 % Allowed : 20.79 % 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: -3.61 (0.30), residues: 530 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.74 (0.23), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS D 50 PHE 0.016 0.004 PHE G 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 93 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 58 time to evaluate : 0.470 Fit side-chains REVERT: A 60 LYS cc_start: 0.6703 (OUTLIER) cc_final: 0.6312 (ttmt) REVERT: A 80 LYS cc_start: 0.8879 (OUTLIER) cc_final: 0.7767 (tmtt) REVERT: B 58 LYS cc_start: 0.7133 (mmtp) cc_final: 0.6531 (mmpt) REVERT: C 60 LYS cc_start: 0.7877 (ttmt) cc_final: 0.6863 (mptm) REVERT: D 60 LYS cc_start: 0.7957 (ttmt) cc_final: 0.7068 (mptm) REVERT: E 58 LYS cc_start: 0.6773 (mmtp) cc_final: 0.6216 (mmpt) REVERT: E 60 LYS cc_start: 0.7018 (OUTLIER) cc_final: 0.6513 (ttmt) REVERT: F 58 LYS cc_start: 0.7217 (mmtp) cc_final: 0.6593 (mmmt) REVERT: F 60 LYS cc_start: 0.7652 (ttmt) cc_final: 0.7003 (ttmt) REVERT: G 58 LYS cc_start: 0.6933 (mmtp) cc_final: 0.6232 (mmpt) REVERT: G 60 LYS cc_start: 0.7791 (ttmt) cc_final: 0.6916 (ttmt) REVERT: H 58 LYS cc_start: 0.6684 (mmtp) cc_final: 0.6400 (mtpt) REVERT: I 58 LYS cc_start: 0.7121 (mmtp) cc_final: 0.6545 (mmpt) REVERT: I 60 LYS cc_start: 0.8108 (ttmt) cc_final: 0.7455 (ttmt) REVERT: J 58 LYS cc_start: 0.6776 (mmtp) cc_final: 0.6053 (mmpt) outliers start: 35 outliers final: 26 residues processed: 82 average time/residue: 1.2285 time to fit residues: 104.1853 Evaluate side-chains 85 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 56 time to evaluate : 0.391 ------------------------------------------------------------------------------- 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 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 59 THR Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 60 LYS 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 61 GLU Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 57 GLU 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 I residue 75 THR Chi-restraints excluded: chain J residue 52 VAL 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: 6.9990 chunk 22 optimal weight: 7.9990 chunk 43 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 chunk 9 optimal weight: 6.9990 chunk 2 optimal weight: 0.9980 chunk 15 optimal weight: 3.9990 chunk 25 optimal weight: 20.0000 chunk 10 optimal weight: 20.0000 chunk 20 optimal weight: 40.0000 chunk 34 optimal weight: 20.0000 overall best weight: 3.1586 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** D 62 GLN ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 99 GLN ** I 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4512 r_free = 0.4512 target = 0.170875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.116471 restraints weight = 4047.698| |-----------------------------------------------------------------------------| r_work (start): 0.3822 rms_B_bonded: 2.74 r_work: 0.3685 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.3548 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 1.4349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 3962 Z= 0.257 Angle : 0.657 5.192 5362 Z= 0.344 Chirality : 0.052 0.151 670 Planarity : 0.002 0.013 676 Dihedral : 12.525 85.932 596 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % 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: -3.53 (0.30), residues: 530 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.68 (0.23), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS E 50 PHE 0.011 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 88 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 59 time to evaluate : 0.434 Fit side-chains REVERT: A 60 LYS cc_start: 0.6733 (OUTLIER) cc_final: 0.6399 (ttmt) REVERT: A 80 LYS cc_start: 0.8840 (OUTLIER) cc_final: 0.7705 (tmtt) REVERT: C 60 LYS cc_start: 0.7918 (ttmt) cc_final: 0.6937 (ttmt) REVERT: D 60 LYS cc_start: 0.7889 (ttmt) cc_final: 0.7049 (mptm) REVERT: E 58 LYS cc_start: 0.6710 (mmtp) cc_final: 0.6075 (mmpt) REVERT: E 60 LYS cc_start: 0.6900 (OUTLIER) cc_final: 0.6591 (ttmt) REVERT: F 49 VAL cc_start: 0.7536 (m) cc_final: 0.7040 (p) REVERT: F 58 LYS cc_start: 0.7115 (mmtp) cc_final: 0.6618 (mmmt) REVERT: F 60 LYS cc_start: 0.7592 (ttmt) cc_final: 0.7038 (ttmt) REVERT: G 58 LYS cc_start: 0.6973 (mmtp) cc_final: 0.6204 (mmpt) REVERT: G 60 LYS cc_start: 0.7692 (ttmt) cc_final: 0.6701 (mptm) REVERT: H 58 LYS cc_start: 0.6630 (mmtp) cc_final: 0.6300 (mtpt) REVERT: I 58 LYS cc_start: 0.7185 (mmtp) cc_final: 0.6623 (mmpt) REVERT: I 60 LYS cc_start: 0.7967 (ttmt) cc_final: 0.7401 (ttmt) REVERT: J 58 LYS cc_start: 0.6792 (mmtp) cc_final: 0.6120 (mmpt) outliers start: 29 outliers final: 24 residues processed: 81 average time/residue: 1.1710 time to fit residues: 98.1345 Evaluate side-chains 81 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 54 time to evaluate : 0.439 ------------------------------------------------------------------------------- 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 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 75 THR Chi-restraints excluded: chain D residue 81 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 57 GLU 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 I residue 75 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 14 optimal weight: 10.0000 chunk 45 optimal weight: 2.9990 chunk 26 optimal weight: 8.9990 chunk 49 optimal weight: 10.0000 chunk 29 optimal weight: 20.0000 chunk 21 optimal weight: 10.0000 chunk 37 optimal weight: 9.9990 chunk 44 optimal weight: 0.2980 chunk 2 optimal weight: 8.9990 chunk 11 optimal weight: 10.0000 chunk 34 optimal weight: 7.9990 overall best weight: 5.8588 ------------------------------------------------------------------------------- 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 ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 62 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 = 0.4477 r_free = 0.4477 target = 0.168101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.113615 restraints weight = 4108.996| |-----------------------------------------------------------------------------| r_work (start): 0.3772 rms_B_bonded: 2.72 r_work: 0.3632 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.3497 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 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 : 0.006 0.050 3962 Z= 0.444 Angle : 0.809 5.612 5362 Z= 0.427 Chirality : 0.057 0.175 670 Planarity : 0.003 0.021 676 Dihedral : 12.869 86.499 596 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.87 % Favored : 91.13 % Rotamer: Outliers : 8.16 % Allowed : 22.63 % Favored : 69.21 % 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: -3.58 (0.30), 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 0.003 0.001 HIS D 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 88 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 57 time to evaluate : 0.415 Fit side-chains REVERT: A 60 LYS cc_start: 0.6699 (OUTLIER) cc_final: 0.6313 (ttmt) REVERT: A 80 LYS cc_start: 0.8882 (OUTLIER) cc_final: 0.7777 (tmtt) REVERT: B 58 LYS cc_start: 0.7093 (mmtp) cc_final: 0.6529 (mmpt) REVERT: C 58 LYS cc_start: 0.7051 (mmtp) cc_final: 0.6691 (mmmt) REVERT: C 60 LYS cc_start: 0.7879 (ttmt) cc_final: 0.6928 (ttmt) REVERT: D 60 LYS cc_start: 0.7903 (ttmt) cc_final: 0.7065 (mmtm) REVERT: E 58 LYS cc_start: 0.6756 (mmtp) cc_final: 0.6147 (mmpt) REVERT: E 60 LYS cc_start: 0.7012 (OUTLIER) cc_final: 0.6608 (ttmt) REVERT: F 49 VAL cc_start: 0.7574 (m) cc_final: 0.7070 (p) REVERT: F 58 LYS cc_start: 0.7135 (mmtp) cc_final: 0.6551 (mmmt) REVERT: F 60 LYS cc_start: 0.7663 (ttmt) cc_final: 0.7016 (ttmt) REVERT: G 58 LYS cc_start: 0.6991 (mmtp) cc_final: 0.6275 (mmpt) REVERT: G 60 LYS cc_start: 0.7791 (ttmt) cc_final: 0.6893 (ttmt) REVERT: H 58 LYS cc_start: 0.6601 (mmtp) cc_final: 0.6248 (mtpt) REVERT: I 58 LYS cc_start: 0.7067 (mmtp) cc_final: 0.6538 (mmpt) REVERT: I 60 LYS cc_start: 0.8037 (ttmt) cc_final: 0.7447 (ttmt) REVERT: J 58 LYS cc_start: 0.6704 (mmtp) cc_final: 0.6047 (mmpt) outliers start: 31 outliers final: 26 residues processed: 78 average time/residue: 1.1404 time to fit residues: 92.2179 Evaluate side-chains 86 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 57 time to evaluate : 0.436 ------------------------------------------------------------------------------- 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 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 59 THR Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 60 LYS 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 61 GLU Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 57 GLU 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 I residue 75 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 2 optimal weight: 8.9990 chunk 22 optimal weight: 3.9990 chunk 7 optimal weight: 0.9980 chunk 0 optimal weight: 30.0000 chunk 5 optimal weight: 9.9990 chunk 28 optimal weight: 4.9990 chunk 8 optimal weight: 0.1980 chunk 44 optimal weight: 9.9990 chunk 21 optimal weight: 0.4980 chunk 17 optimal weight: 7.9990 chunk 6 optimal weight: 3.9990 overall best weight: 1.9384 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** C 62 GLN E 62 GLN F 99 GLN H 99 GLN I 62 GLN J 62 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4541 r_free = 0.4541 target = 0.172733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.118500 restraints weight = 4040.096| |-----------------------------------------------------------------------------| r_work (start): 0.3861 rms_B_bonded: 2.71 r_work: 0.3720 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 1.4406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3962 Z= 0.182 Angle : 0.596 5.025 5362 Z= 0.311 Chirality : 0.051 0.148 670 Planarity : 0.002 0.018 676 Dihedral : 12.402 89.951 596 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 6.84 % Allowed : 24.74 % Favored : 68.42 % 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 0.003 0.000 HIS E 50 PHE 0.009 0.002 PHE G 94 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3147.57 seconds wall clock time: 56 minutes 25.66 seconds (3385.66 seconds total)