Starting phenix.real_space_refine on Wed Oct 9 17:44:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x7q_38107/10_2024/8x7q_38107.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x7q_38107/10_2024/8x7q_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x7q_38107/10_2024/8x7q_38107.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x7q_38107/10_2024/8x7q_38107.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x7q_38107/10_2024/8x7q_38107.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x7q_38107/10_2024/8x7q_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-5477/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: 2.86, per 1000 atoms: 0.73 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: 1.00 Conformation dependent library (CDL) restraints added in 494.6 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: 0.60 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: 0.98 Time building geometry restraints manager: 1.06 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 45 through 99) selection = (chain 'B' and resid 45 through 99) selection = (chain 'C' and resid 45 through 99) selection = (chain 'D' and resid 45 through 99) selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.780 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: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.880 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.030 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:11.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.510 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 0 poor density : 45 time to evaluate : 0.409 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: 1.3734 time to fit residues: 64.1469 Evaluate side-chains 23 residues out of total 380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 23 time to evaluate : 0.464 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4517 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 fitting. rotamer outliers: 25 poor density : 88 time to evaluate : 0.421 Fit side-chains revert: symmetry clash REVERT: A 49 VAL cc_start: 0.3783 (OUTLIER) cc_final: 0.3365 (p) REVERT: A 58 LYS cc_start: 0.6250 (mmtp) cc_final: 0.5923 (mmmt) REVERT: A 62 GLN cc_start: 0.7443 (mt0) cc_final: 0.7210 (mt0) REVERT: B 96 LYS cc_start: 0.7314 (mtpt) cc_final: 0.7083 (mtpm) REVERT: C 64 THR cc_start: 0.7415 (m) cc_final: 0.7122 (m) REVERT: C 99 GLN cc_start: 0.4288 (tm-30) cc_final: 0.3672 (mt0) REVERT: D 62 GLN cc_start: 0.7341 (mt0) cc_final: 0.6912 (mt0) REVERT: F 49 VAL cc_start: 0.5728 (OUTLIER) cc_final: 0.5013 (p) REVERT: F 57 GLU cc_start: 0.6758 (mp0) cc_final: 0.6068 (pt0) REVERT: F 60 LYS cc_start: 0.5079 (ttmt) cc_final: 0.4712 (mptm) REVERT: F 61 GLU cc_start: 0.6491 (OUTLIER) cc_final: 0.5848 (pm20) REVERT: F 83 GLU cc_start: 0.6720 (mt-10) cc_final: 0.6474 (mt-10) REVERT: F 98 ASP cc_start: 0.6015 (m-30) cc_final: 0.5475 (m-30) REVERT: G 49 VAL cc_start: 0.5299 (OUTLIER) cc_final: 0.4695 (p) REVERT: G 83 GLU cc_start: 0.6795 (mt-10) cc_final: 0.6437 (mt-10) REVERT: H 57 GLU cc_start: 0.6209 (OUTLIER) cc_final: 0.5695 (pp20) REVERT: H 75 THR cc_start: 0.7642 (m) cc_final: 0.7424 (m) REVERT: I 60 LYS cc_start: 0.6643 (ttmt) cc_final: 0.6178 (tppt) REVERT: I 96 LYS cc_start: 0.6084 (tttp) cc_final: 0.5858 (tttm) REVERT: J 60 LYS cc_start: 0.5770 (ttmt) cc_final: 0.5522 (ttmt) outliers start: 25 outliers final: 7 residues processed: 104 average time/residue: 1.2724 time to fit residues: 136.5717 Evaluate side-chains 78 residues out of total 380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 66 time to evaluate : 0.445 ------------------------------------------------------------------------------- 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 H residue 57 GLU 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 25 optimal weight: 20.0000 chunk 14 optimal weight: 0.4980 chunk 37 optimal weight: 0.0980 chunk 30 optimal weight: 0.7980 chunk 12 optimal weight: 5.9990 chunk 45 optimal weight: 20.0000 chunk 49 optimal weight: 10.0000 chunk 40 optimal weight: 10.0000 chunk 15 optimal weight: 7.9990 chunk 36 optimal weight: 10.0000 chunk 44 optimal weight: 1.9990 overall best weight: 1.8784 ------------------------------------------------------------------------------- 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 F 99 GLN G 62 GLN G 99 GLN I 65 ASN I 79 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4842 moved from start: 1.1920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3962 Z= 0.208 Angle : 0.648 4.835 5362 Z= 0.352 Chirality : 0.053 0.174 670 Planarity : 0.003 0.015 676 Dihedral : 12.731 83.286 596 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 6.32 % Allowed : 22.89 % 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: -3.46 (0.28), residues: 530 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.63 (0.22), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 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 104 residues out of total 380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 80 time to evaluate : 0.407 Fit side-chains REVERT: A 58 LYS cc_start: 0.6277 (mmtp) cc_final: 0.5568 (mmpt) REVERT: A 62 GLN cc_start: 0.7820 (mt0) cc_final: 0.7539 (mt0) REVERT: A 79 GLN cc_start: 0.8851 (OUTLIER) cc_final: 0.8447 (mt0) REVERT: A 83 GLU cc_start: 0.6604 (mt-10) cc_final: 0.6022 (mt-10) REVERT: B 83 GLU cc_start: 0.7211 (mt-10) cc_final: 0.6755 (mt-10) REVERT: C 60 LYS cc_start: 0.5205 (ttmt) cc_final: 0.4751 (mmtp) REVERT: C 99 GLN cc_start: 0.4002 (tm-30) cc_final: 0.3518 (mt0) REVERT: D 62 GLN cc_start: 0.7228 (mt0) cc_final: 0.6641 (mt0) REVERT: D 96 LYS cc_start: 0.7172 (ttpt) cc_final: 0.6895 (tttp) REVERT: E 79 GLN cc_start: 0.8614 (OUTLIER) cc_final: 0.8386 (mt0) REVERT: F 58 LYS cc_start: 0.5551 (mmtp) cc_final: 0.4990 (mtpt) REVERT: F 83 GLU cc_start: 0.6867 (mt-10) cc_final: 0.6462 (mt-10) REVERT: G 57 GLU cc_start: 0.6204 (OUTLIER) cc_final: 0.5920 (pt0) REVERT: G 99 GLN cc_start: 0.4061 (mt0) cc_final: 0.3773 (mt0) REVERT: H 60 LYS cc_start: 0.6013 (ttmt) cc_final: 0.5523 (ttmt) REVERT: I 58 LYS cc_start: 0.6009 (mmtp) cc_final: 0.5111 (mmpt) REVERT: I 60 LYS cc_start: 0.6730 (ttmt) cc_final: 0.6505 (ttmt) REVERT: I 72 THR cc_start: 0.7575 (OUTLIER) cc_final: 0.7364 (p) REVERT: I 75 THR cc_start: 0.7609 (OUTLIER) cc_final: 0.7358 (m) REVERT: J 60 LYS cc_start: 0.5813 (ttmt) cc_final: 0.5573 (ttmt) REVERT: J 79 GLN cc_start: 0.8233 (OUTLIER) cc_final: 0.7615 (mt0) outliers start: 24 outliers final: 6 residues processed: 94 average time/residue: 1.4478 time to fit residues: 139.7636 Evaluate side-chains 76 residues out of total 380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 64 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 79 GLN 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 H residue 52 VAL Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 75 THR 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 34 optimal weight: 20.0000 chunk 23 optimal weight: 9.9990 chunk 5 optimal weight: 10.0000 chunk 21 optimal weight: 20.0000 chunk 30 optimal weight: 30.0000 chunk 45 optimal weight: 20.0000 chunk 48 optimal weight: 1.9990 chunk 43 optimal weight: 6.9990 chunk 13 optimal weight: 6.9990 chunk 40 optimal weight: 10.0000 chunk 27 optimal weight: 9.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 62 GLN C 62 GLN C 79 GLN D 79 GLN F 62 GLN F 99 GLN G 62 GLN H 99 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5029 moved from start: 1.3558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.079 3962 Z= 0.542 Angle : 0.942 6.843 5362 Z= 0.494 Chirality : 0.060 0.174 670 Planarity : 0.004 0.018 676 Dihedral : 12.566 76.187 596 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.36 % Favored : 92.64 % Rotamer: Outliers : 12.63 % Allowed : 16.84 % 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: -3.63 (0.28), residues: 530 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.76 (0.22), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS E 50 PHE 0.017 0.004 PHE G 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 115 residues out of total 380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 67 time to evaluate : 0.461 Fit side-chains REVERT: A 58 LYS cc_start: 0.6083 (mmtp) cc_final: 0.5416 (mmmt) REVERT: A 60 LYS cc_start: 0.5859 (ttmt) cc_final: 0.5546 (ttmt) REVERT: A 79 GLN cc_start: 0.8225 (OUTLIER) cc_final: 0.7878 (mt0) REVERT: B 79 GLN cc_start: 0.8179 (OUTLIER) cc_final: 0.7559 (mt0) REVERT: C 60 LYS cc_start: 0.5268 (ttmt) cc_final: 0.4683 (mptm) REVERT: D 60 LYS cc_start: 0.5110 (ttmt) cc_final: 0.4712 (mmtm) REVERT: D 62 GLN cc_start: 0.7601 (mt0) cc_final: 0.7097 (mt0) REVERT: E 58 LYS cc_start: 0.5490 (mmtp) cc_final: 0.4858 (mmpt) REVERT: F 58 LYS cc_start: 0.5821 (mmtp) cc_final: 0.4988 (mmpt) REVERT: G 58 LYS cc_start: 0.5474 (mmtp) cc_final: 0.4749 (mmpt) REVERT: G 60 LYS cc_start: 0.5105 (ttmt) cc_final: 0.4528 (mptm) REVERT: G 79 GLN cc_start: 0.8270 (OUTLIER) cc_final: 0.7829 (mt0) REVERT: H 58 LYS cc_start: 0.6328 (mmtp) cc_final: 0.5804 (mtpt) REVERT: H 98 ASP cc_start: 0.7184 (m-30) cc_final: 0.6814 (m-30) REVERT: I 58 LYS cc_start: 0.6279 (mmtp) cc_final: 0.5565 (mmpt) REVERT: I 60 LYS cc_start: 0.6751 (ttmt) cc_final: 0.6279 (ttmt) REVERT: I 75 THR cc_start: 0.7740 (OUTLIER) cc_final: 0.7445 (m) REVERT: I 98 ASP cc_start: 0.6867 (m-30) cc_final: 0.6635 (m-30) REVERT: J 58 LYS cc_start: 0.5900 (mmtp) cc_final: 0.5116 (mmpt) REVERT: J 60 LYS cc_start: 0.5578 (ttmt) cc_final: 0.5214 (ttmt) REVERT: J 79 GLN cc_start: 0.8393 (OUTLIER) cc_final: 0.8091 (mt0) outliers start: 48 outliers final: 25 residues processed: 100 average time/residue: 1.4363 time to fit residues: 147.7978 Evaluate side-chains 92 residues out of total 380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 62 time to evaluate : 0.669 ------------------------------------------------------------------------------- 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 B residue 62 GLN Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 79 GLN Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain F residue 96 LYS 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 79 GLN Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 57 GLU Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain I residue 75 THR Chi-restraints excluded: chain J residue 52 VAL Chi-restraints excluded: chain J residue 75 THR Chi-restraints excluded: chain J residue 79 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 0 optimal weight: 20.0000 chunk 35 optimal weight: 9.9990 chunk 19 optimal weight: 9.9990 chunk 41 optimal weight: 7.9990 chunk 33 optimal weight: 6.9990 chunk 24 optimal weight: 10.0000 chunk 43 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 16 optimal weight: 4.9990 chunk 9 optimal weight: 9.9990 chunk 28 optimal weight: 0.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 62 GLN C 62 GLN C 99 GLN F 99 GLN H 99 GLN I 62 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5042 moved from start: 1.3727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 3962 Z= 0.292 Angle : 0.710 4.803 5362 Z= 0.375 Chirality : 0.053 0.159 670 Planarity : 0.003 0.015 676 Dihedral : 12.155 72.232 596 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 10.53 % Allowed : 18.95 % 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: -3.60 (0.29), residues: 530 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.73 (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 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 104 residues out of total 380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 64 time to evaluate : 0.584 Fit side-chains REVERT: A 58 LYS cc_start: 0.6035 (mmtp) cc_final: 0.5405 (mmpt) REVERT: A 60 LYS cc_start: 0.5716 (ttmt) cc_final: 0.5337 (ttmt) REVERT: A 62 GLN cc_start: 0.7798 (mt0) cc_final: 0.7484 (mt0) REVERT: A 79 GLN cc_start: 0.8262 (OUTLIER) cc_final: 0.7957 (mt0) REVERT: C 60 LYS cc_start: 0.5323 (ttmt) cc_final: 0.4758 (mptm) REVERT: D 60 LYS cc_start: 0.5373 (ttmt) cc_final: 0.4871 (mmtm) REVERT: D 62 GLN cc_start: 0.7539 (mt0) cc_final: 0.6989 (mt0) REVERT: E 58 LYS cc_start: 0.5552 (mmtp) cc_final: 0.4921 (mmpt) REVERT: E 62 GLN cc_start: 0.7747 (mt0) cc_final: 0.7441 (mt0) REVERT: F 58 LYS cc_start: 0.5902 (mmtp) cc_final: 0.5289 (mmmt) REVERT: G 49 VAL cc_start: 0.6161 (m) cc_final: 0.5743 (p) REVERT: G 58 LYS cc_start: 0.5504 (mmtp) cc_final: 0.4816 (mmpt) REVERT: G 60 LYS cc_start: 0.5086 (ttmt) cc_final: 0.4478 (tptm) REVERT: G 79 GLN cc_start: 0.8184 (OUTLIER) cc_final: 0.7911 (mt0) REVERT: H 58 LYS cc_start: 0.6471 (mmtp) cc_final: 0.5899 (mtpt) REVERT: I 58 LYS cc_start: 0.6312 (mmtp) cc_final: 0.5593 (mmpt) REVERT: I 60 LYS cc_start: 0.6727 (ttmt) cc_final: 0.6256 (ttmt) REVERT: I 72 THR cc_start: 0.7605 (m) cc_final: 0.7337 (p) REVERT: I 75 THR cc_start: 0.7683 (OUTLIER) cc_final: 0.7381 (m) REVERT: J 58 LYS cc_start: 0.6070 (mmtp) cc_final: 0.5243 (mmpt) REVERT: J 60 LYS cc_start: 0.5593 (ttmt) cc_final: 0.5203 (ttmt) REVERT: J 62 GLN cc_start: 0.7870 (mt0) cc_final: 0.7488 (mt0) outliers start: 40 outliers final: 24 residues processed: 91 average time/residue: 1.4810 time to fit residues: 138.8009 Evaluate side-chains 87 residues out of total 380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 60 time to evaluate : 0.488 ------------------------------------------------------------------------------- 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 B residue 62 GLN Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 79 GLN Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 61 GLU Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 79 GLN Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 57 GLU Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain H residue 81 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 11 optimal weight: 7.9990 chunk 48 optimal weight: 1.9990 chunk 40 optimal weight: 20.0000 chunk 22 optimal weight: 6.9990 chunk 4 optimal weight: 6.9990 chunk 16 optimal weight: 0.9990 chunk 25 optimal weight: 20.0000 chunk 46 optimal weight: 4.9990 chunk 5 optimal weight: 9.9990 chunk 27 optimal weight: 2.9990 chunk 35 optimal weight: 0.0670 overall best weight: 2.2126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 62 GLN ** C 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 GLN D 99 GLN F 99 GLN H 99 GLN I 62 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5034 moved from start: 1.3813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 3962 Z= 0.190 Angle : 0.598 4.620 5362 Z= 0.313 Chirality : 0.051 0.151 670 Planarity : 0.002 0.014 676 Dihedral : 11.708 74.697 596 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 8.68 % Allowed : 19.47 % Favored : 71.84 % 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 (0.30), residues: 530 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.63 (0.23), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 50 PHE 0.010 0.002 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 96 residues out of total 380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 63 time to evaluate : 0.415 Fit side-chains REVERT: A 58 LYS cc_start: 0.6070 (mmtp) cc_final: 0.5379 (mmmt) REVERT: A 60 LYS cc_start: 0.5602 (ttmt) cc_final: 0.5235 (ttmt) REVERT: A 62 GLN cc_start: 0.7792 (mt0) cc_final: 0.7334 (mt0) REVERT: A 79 GLN cc_start: 0.8175 (OUTLIER) cc_final: 0.7823 (mt0) REVERT: A 80 LYS cc_start: 0.6814 (OUTLIER) cc_final: 0.5720 (tmtt) REVERT: B 62 GLN cc_start: 0.8208 (OUTLIER) cc_final: 0.7940 (pm20) REVERT: C 60 LYS cc_start: 0.5212 (ttmt) cc_final: 0.4741 (ttmt) REVERT: D 60 LYS cc_start: 0.5494 (ttmt) cc_final: 0.4987 (mmtm) REVERT: D 62 GLN cc_start: 0.7595 (mt0) cc_final: 0.6986 (mt0) REVERT: D 99 GLN cc_start: 0.4777 (mt0) cc_final: 0.4561 (mt0) REVERT: E 49 VAL cc_start: 0.5819 (m) cc_final: 0.5349 (p) REVERT: E 58 LYS cc_start: 0.5514 (mmtp) cc_final: 0.4904 (mmpt) REVERT: F 58 LYS cc_start: 0.5882 (mmtp) cc_final: 0.4845 (mmpt) REVERT: G 58 LYS cc_start: 0.5448 (mmtp) cc_final: 0.4753 (mmpt) REVERT: G 60 LYS cc_start: 0.5044 (ttmt) cc_final: 0.4445 (tptm) REVERT: G 79 GLN cc_start: 0.8085 (OUTLIER) cc_final: 0.7737 (mt0) REVERT: H 57 GLU cc_start: 0.6418 (OUTLIER) cc_final: 0.5461 (pp20) REVERT: H 58 LYS cc_start: 0.6412 (mmtp) cc_final: 0.5755 (mmpt) REVERT: I 58 LYS cc_start: 0.6433 (mmtp) cc_final: 0.5629 (mmpt) REVERT: I 60 LYS cc_start: 0.6766 (ttmt) cc_final: 0.6318 (ttmt) REVERT: I 72 THR cc_start: 0.7586 (OUTLIER) cc_final: 0.7361 (p) REVERT: I 75 THR cc_start: 0.7663 (OUTLIER) cc_final: 0.7371 (m) REVERT: J 58 LYS cc_start: 0.6036 (mmtp) cc_final: 0.5275 (mmpt) REVERT: J 60 LYS cc_start: 0.5474 (ttmt) cc_final: 0.5121 (ttmt) REVERT: J 62 GLN cc_start: 0.7817 (mt0) cc_final: 0.7538 (mt0) outliers start: 33 outliers final: 17 residues processed: 83 average time/residue: 1.4120 time to fit residues: 120.7967 Evaluate side-chains 85 residues out of total 380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 61 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 79 GLN Chi-restraints excluded: chain A residue 80 LYS Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 62 GLN Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 79 GLN Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 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 G residue 79 GLN Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 57 GLU Chi-restraints excluded: chain H residue 96 LYS Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 75 THR 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 27 optimal weight: 5.9990 chunk 40 optimal weight: 20.0000 chunk 48 optimal weight: 7.9990 chunk 30 optimal weight: 20.0000 chunk 29 optimal weight: 20.0000 chunk 22 optimal weight: 6.9990 chunk 19 optimal weight: 20.0000 chunk 28 optimal weight: 8.9990 chunk 14 optimal weight: 0.9990 chunk 9 optimal weight: 0.0670 chunk 32 optimal weight: 3.9990 overall best weight: 3.6126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 62 GLN C 62 GLN F 99 GLN G 62 GLN H 99 GLN I 62 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5049 moved from start: 1.3975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 3962 Z= 0.282 Angle : 0.678 4.877 5362 Z= 0.355 Chirality : 0.053 0.157 670 Planarity : 0.002 0.013 676 Dihedral : 12.043 78.469 596 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 9.47 % Allowed : 18.68 % Favored : 71.84 % 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: -3.50 (0.30), residues: 530 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.66 (0.23), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS D 50 PHE 0.012 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 97 residues out of total 380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 61 time to evaluate : 0.437 Fit side-chains REVERT: A 58 LYS cc_start: 0.6037 (mmtp) cc_final: 0.5473 (mmpt) REVERT: A 60 LYS cc_start: 0.5359 (ttmt) cc_final: 0.5119 (ttmt) REVERT: A 62 GLN cc_start: 0.7852 (mt0) cc_final: 0.7506 (mt0) REVERT: A 79 GLN cc_start: 0.8207 (OUTLIER) cc_final: 0.7736 (mt0) REVERT: A 80 LYS cc_start: 0.6792 (OUTLIER) cc_final: 0.5726 (tmtt) REVERT: C 60 LYS cc_start: 0.5236 (ttmt) cc_final: 0.4753 (ttmt) REVERT: D 60 LYS cc_start: 0.5425 (ttmt) cc_final: 0.5005 (mmtm) REVERT: D 62 GLN cc_start: 0.7581 (mt0) cc_final: 0.7029 (mt0) REVERT: E 58 LYS cc_start: 0.5576 (mmtp) cc_final: 0.5025 (mmpt) REVERT: E 62 GLN cc_start: 0.7688 (mt0) cc_final: 0.7400 (mt0) REVERT: F 58 LYS cc_start: 0.5823 (mmtp) cc_final: 0.5235 (mmmt) REVERT: G 58 LYS cc_start: 0.5510 (mmtp) cc_final: 0.4843 (mmpt) REVERT: G 60 LYS cc_start: 0.5145 (ttmt) cc_final: 0.4561 (mptm) REVERT: G 79 GLN cc_start: 0.8146 (OUTLIER) cc_final: 0.7924 (mt0) REVERT: H 58 LYS cc_start: 0.6086 (mmtp) cc_final: 0.5450 (mmpt) REVERT: I 58 LYS cc_start: 0.6385 (mmtp) cc_final: 0.5625 (mmpt) REVERT: I 60 LYS cc_start: 0.6699 (ttmt) cc_final: 0.6217 (ttmt) REVERT: I 72 THR cc_start: 0.7581 (OUTLIER) cc_final: 0.7316 (p) REVERT: I 75 THR cc_start: 0.7707 (OUTLIER) cc_final: 0.7405 (m) REVERT: J 58 LYS cc_start: 0.6019 (mmtp) cc_final: 0.5241 (mmpt) REVERT: J 60 LYS cc_start: 0.5501 (ttmt) cc_final: 0.5166 (ttmt) REVERT: J 62 GLN cc_start: 0.7867 (mt0) cc_final: 0.7512 (mt0) outliers start: 36 outliers final: 26 residues processed: 85 average time/residue: 1.3283 time to fit residues: 116.2625 Evaluate side-chains 94 residues out of total 380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 63 time to evaluate : 0.416 ------------------------------------------------------------------------------- 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 A residue 80 LYS Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 79 GLN Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain D residue 75 THR 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 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 75 THR Chi-restraints excluded: chain G residue 79 GLN Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 57 GLU Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 75 THR Chi-restraints excluded: chain I residue 99 GLN 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 23 optimal weight: 4.9990 chunk 4 optimal weight: 20.0000 chunk 37 optimal weight: 7.9990 chunk 43 optimal weight: 2.9990 chunk 46 optimal weight: 0.0060 chunk 42 optimal weight: 5.9990 chunk 44 optimal weight: 8.9990 chunk 27 optimal weight: 2.9990 chunk 19 optimal weight: 20.0000 chunk 35 optimal weight: 0.0570 chunk 13 optimal weight: 4.9990 overall best weight: 2.2120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 62 GLN ** 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5047 moved from start: 1.4058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.016 3962 Z= 0.188 Angle : 0.580 4.729 5362 Z= 0.304 Chirality : 0.051 0.150 670 Planarity : 0.002 0.013 676 Dihedral : 11.763 83.859 596 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 8.68 % Allowed : 19.47 % Favored : 71.84 % 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: -3.39 (0.31), residues: 530 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.58 (0.23), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 50 PHE 0.009 0.002 PHE E 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 fitting. rotamer outliers: 33 poor density : 59 time to evaluate : 0.428 Fit side-chains REVERT: A 60 LYS cc_start: 0.5423 (ttmt) cc_final: 0.5215 (ttmt) REVERT: A 62 GLN cc_start: 0.7864 (mt0) cc_final: 0.7476 (mt0) REVERT: A 79 GLN cc_start: 0.8140 (OUTLIER) cc_final: 0.7775 (mt0) REVERT: A 80 LYS cc_start: 0.6756 (OUTLIER) cc_final: 0.5691 (tmtt) REVERT: C 60 LYS cc_start: 0.5245 (ttmt) cc_final: 0.4772 (ttmt) REVERT: D 60 LYS cc_start: 0.5574 (ttmt) cc_final: 0.5074 (mmtm) REVERT: D 62 GLN cc_start: 0.7631 (mt0) cc_final: 0.7066 (mt0) REVERT: E 58 LYS cc_start: 0.5581 (mmtp) cc_final: 0.5068 (mmpt) REVERT: F 58 LYS cc_start: 0.5841 (mmtp) cc_final: 0.4856 (mmpt) REVERT: G 58 LYS cc_start: 0.5658 (mmtp) cc_final: 0.5003 (mmpt) REVERT: G 60 LYS cc_start: 0.5096 (ttmt) cc_final: 0.4604 (ttmt) REVERT: G 79 GLN cc_start: 0.8090 (OUTLIER) cc_final: 0.7742 (mt0) REVERT: H 58 LYS cc_start: 0.6079 (mmtp) cc_final: 0.5402 (mmpt) REVERT: I 58 LYS cc_start: 0.6376 (mmtp) cc_final: 0.5624 (mmpt) REVERT: I 60 LYS cc_start: 0.6707 (ttmt) cc_final: 0.6261 (ttmt) REVERT: I 72 THR cc_start: 0.7562 (OUTLIER) cc_final: 0.7351 (p) REVERT: I 75 THR cc_start: 0.7695 (OUTLIER) cc_final: 0.7434 (m) REVERT: J 58 LYS cc_start: 0.6026 (mmtp) cc_final: 0.5278 (mmpt) REVERT: J 60 LYS cc_start: 0.5521 (ttmt) cc_final: 0.5194 (ttmt) REVERT: J 62 GLN cc_start: 0.7824 (mt0) cc_final: 0.7572 (mt0) outliers start: 33 outliers final: 25 residues processed: 79 average time/residue: 1.4809 time to fit residues: 120.3642 Evaluate side-chains 86 residues out of total 380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 56 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 79 GLN Chi-restraints excluded: chain A residue 80 LYS Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 62 GLN Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 79 GLN Chi-restraints excluded: chain B residue 96 LYS 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 52 VAL 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 G residue 79 GLN Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 57 GLU Chi-restraints excluded: chain H residue 96 LYS Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 75 THR Chi-restraints excluded: chain I residue 99 GLN 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 40 optimal weight: 20.0000 chunk 42 optimal weight: 0.0370 chunk 44 optimal weight: 9.9990 chunk 29 optimal weight: 20.0000 chunk 47 optimal weight: 2.9990 chunk 28 optimal weight: 10.0000 chunk 22 optimal weight: 8.9990 chunk 33 optimal weight: 4.9990 chunk 49 optimal weight: 20.0000 chunk 45 optimal weight: 7.9990 chunk 39 optimal weight: 5.9990 overall best weight: 4.4066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 62 GLN C 62 GLN F 99 GLN G 62 GLN H 99 GLN I 62 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5063 moved from start: 1.4172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 3962 Z= 0.338 Angle : 0.714 5.075 5362 Z= 0.375 Chirality : 0.054 0.150 670 Planarity : 0.003 0.014 676 Dihedral : 12.324 87.204 596 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 10.00 % Allowed : 18.68 % Favored : 71.32 % 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 (0.30), residues: 530 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.65 (0.23), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS E 50 PHE 0.013 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 98 residues out of total 380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 60 time to evaluate : 0.540 Fit side-chains REVERT: A 58 LYS cc_start: 0.6131 (mmtp) cc_final: 0.5549 (mmpt) REVERT: A 60 LYS cc_start: 0.5382 (ttmt) cc_final: 0.5100 (ttmt) REVERT: A 62 GLN cc_start: 0.7872 (mt0) cc_final: 0.7580 (mt0) REVERT: A 79 GLN cc_start: 0.8271 (OUTLIER) cc_final: 0.7872 (mt0) REVERT: A 80 LYS cc_start: 0.6777 (OUTLIER) cc_final: 0.5714 (tmtt) REVERT: C 60 LYS cc_start: 0.5285 (ttmt) cc_final: 0.4787 (ttmt) REVERT: D 60 LYS cc_start: 0.5565 (ttmt) cc_final: 0.5080 (mmtm) REVERT: D 62 GLN cc_start: 0.7656 (mt0) cc_final: 0.7148 (mt0) REVERT: E 58 LYS cc_start: 0.5508 (mmtp) cc_final: 0.4971 (mmpt) REVERT: E 62 GLN cc_start: 0.7700 (mt0) cc_final: 0.7466 (mt0) REVERT: F 58 LYS cc_start: 0.5658 (mmtp) cc_final: 0.5097 (mmmt) REVERT: G 57 GLU cc_start: 0.6397 (OUTLIER) cc_final: 0.6185 (tm-30) REVERT: G 58 LYS cc_start: 0.5481 (mmtp) cc_final: 0.4989 (mmpt) REVERT: G 60 LYS cc_start: 0.5150 (ttmt) cc_final: 0.4675 (ttmt) REVERT: G 79 GLN cc_start: 0.8194 (OUTLIER) cc_final: 0.7977 (mt0) REVERT: H 58 LYS cc_start: 0.6021 (mmtp) cc_final: 0.5204 (mmpt) REVERT: I 58 LYS cc_start: 0.6360 (mmtp) cc_final: 0.5632 (mmpt) REVERT: I 60 LYS cc_start: 0.6758 (ttmt) cc_final: 0.6230 (ttmt) REVERT: I 72 THR cc_start: 0.7562 (OUTLIER) cc_final: 0.7300 (p) REVERT: I 75 THR cc_start: 0.7595 (OUTLIER) cc_final: 0.7306 (m) REVERT: J 58 LYS cc_start: 0.5957 (mmtp) cc_final: 0.5210 (mmpt) REVERT: J 60 LYS cc_start: 0.5460 (ttmt) cc_final: 0.5135 (ttmt) outliers start: 38 outliers final: 27 residues processed: 84 average time/residue: 1.3967 time to fit residues: 121.1663 Evaluate side-chains 91 residues out of total 380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 58 time to evaluate : 0.457 ------------------------------------------------------------------------------- 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 A residue 80 LYS Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 62 GLN Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 79 GLN Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain D residue 75 THR 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 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 57 GLU Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 79 GLN Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 57 GLU Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 75 THR Chi-restraints excluded: chain I residue 99 GLN 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 4 optimal weight: 6.9990 chunk 30 optimal weight: 20.0000 chunk 24 optimal weight: 6.9990 chunk 31 optimal weight: 10.0000 chunk 42 optimal weight: 5.9990 chunk 12 optimal weight: 2.9990 chunk 36 optimal weight: 6.9990 chunk 5 optimal weight: 7.9990 chunk 11 optimal weight: 4.9990 chunk 39 optimal weight: 9.9990 chunk 16 optimal weight: 0.0980 overall best weight: 4.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 62 GLN C 62 GLN F 99 GLN H 99 GLN I 62 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5068 moved from start: 1.4236 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= 0.323 Angle : 0.701 4.952 5362 Z= 0.368 Chirality : 0.054 0.151 670 Planarity : 0.003 0.014 676 Dihedral : 12.465 89.162 596 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 9.74 % Allowed : 18.95 % Favored : 71.32 % 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: -3.50 (0.30), residues: 530 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.66 (0.23), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 50 PHE 0.013 0.003 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 101 residues out of total 380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 64 time to evaluate : 0.442 Fit side-chains REVERT: A 58 LYS cc_start: 0.6080 (mmtp) cc_final: 0.5513 (mmpt) REVERT: A 60 LYS cc_start: 0.5424 (ttmt) cc_final: 0.5131 (ttmt) REVERT: A 62 GLN cc_start: 0.7961 (mt0) cc_final: 0.7606 (mt0) REVERT: A 79 GLN cc_start: 0.8208 (OUTLIER) cc_final: 0.7793 (mt0) REVERT: A 80 LYS cc_start: 0.6794 (OUTLIER) cc_final: 0.5752 (tmtt) REVERT: B 62 GLN cc_start: 0.8186 (OUTLIER) cc_final: 0.7889 (pm20) REVERT: C 60 LYS cc_start: 0.5346 (ttmt) cc_final: 0.4827 (ttmt) REVERT: D 60 LYS cc_start: 0.5573 (ttmt) cc_final: 0.5118 (mmtm) REVERT: D 62 GLN cc_start: 0.7755 (mt0) cc_final: 0.7220 (mt0) REVERT: E 58 LYS cc_start: 0.5566 (mmtp) cc_final: 0.5038 (mmpt) REVERT: E 62 GLN cc_start: 0.7675 (mt0) cc_final: 0.7451 (mt0) REVERT: F 58 LYS cc_start: 0.5722 (mmtp) cc_final: 0.5172 (mmmt) REVERT: G 57 GLU cc_start: 0.6392 (OUTLIER) cc_final: 0.6136 (tm-30) REVERT: G 58 LYS cc_start: 0.5520 (mmtp) cc_final: 0.5021 (mmpt) REVERT: G 60 LYS cc_start: 0.5095 (ttmt) cc_final: 0.4617 (ttmt) REVERT: G 79 GLN cc_start: 0.8189 (OUTLIER) cc_final: 0.7972 (mt0) REVERT: H 58 LYS cc_start: 0.5915 (mmtp) cc_final: 0.5096 (mmpt) REVERT: I 58 LYS cc_start: 0.6311 (mmtp) cc_final: 0.5606 (mmpt) REVERT: I 60 LYS cc_start: 0.6806 (ttmt) cc_final: 0.6258 (ttmt) REVERT: I 72 THR cc_start: 0.7570 (OUTLIER) cc_final: 0.7334 (p) REVERT: I 75 THR cc_start: 0.7607 (OUTLIER) cc_final: 0.7321 (m) REVERT: J 58 LYS cc_start: 0.5956 (mmtp) cc_final: 0.5198 (mmpt) REVERT: J 60 LYS cc_start: 0.5433 (ttmt) cc_final: 0.5112 (ttmt) REVERT: J 62 GLN cc_start: 0.7809 (mt0) cc_final: 0.7499 (mt0) outliers start: 37 outliers final: 27 residues processed: 87 average time/residue: 1.2881 time to fit residues: 115.7992 Evaluate side-chains 93 residues out of total 380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 59 time to evaluate : 0.475 ------------------------------------------------------------------------------- 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 A residue 80 LYS Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 62 GLN Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 79 GLN Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain D residue 75 THR 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 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 57 GLU Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 79 GLN Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 57 GLU Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 72 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 40 optimal weight: 20.0000 chunk 5 optimal weight: 0.0070 chunk 7 optimal weight: 6.9990 chunk 34 optimal weight: 20.0000 chunk 2 optimal weight: 3.9990 chunk 28 optimal weight: 4.9990 chunk 45 optimal weight: 5.9990 chunk 26 optimal weight: 8.9990 chunk 1 optimal weight: 5.9990 chunk 31 optimal weight: 3.9990 chunk 30 optimal weight: 20.0000 overall best weight: 3.8006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 62 GLN C 62 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 = 0.4557 r_free = 0.4557 target = 0.172113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.117195 restraints weight = 3804.164| |-----------------------------------------------------------------------------| r_work (start): 0.3856 rms_B_bonded: 2.71 r_work: 0.3704 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.3548 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 1.4285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3962 Z= 0.293 Angle : 0.679 4.886 5362 Z= 0.356 Chirality : 0.053 0.149 670 Planarity : 0.002 0.014 676 Dihedral : 12.405 88.215 596 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 9.74 % Allowed : 18.95 % Favored : 71.32 % 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: -3.50 (0.31), residues: 530 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.66 (0.23), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 50 PHE 0.012 0.003 PHE G 94 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2221.25 seconds wall clock time: 52 minutes 23.02 seconds (3143.02 seconds total)