Starting phenix.real_space_refine on Wed Feb 14 16:40:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x57_33010/02_2024/7x57_33010.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x57_33010/02_2024/7x57_33010.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.63 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x57_33010/02_2024/7x57_33010.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x57_33010/02_2024/7x57_33010.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x57_33010/02_2024/7x57_33010.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x57_33010/02_2024/7x57_33010.pdb" } resolution = 3.63 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= -0.000 sd= 1.000 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: 5 Type Number sf(0) Gaussians P 242 5.49 5 S 20 5.16 5 C 5373 2.51 5 N 1845 2.21 5 O 2287 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 63": "NH1" <-> "NH2" Residue "A ARG 72": "NH1" <-> "NH2" Residue "A ARG 128": "NH1" <-> "NH2" Residue "A ARG 131": "NH1" <-> "NH2" Residue "A ARG 134": "NH1" <-> "NH2" Residue "B ARG 39": "NH1" <-> "NH2" Residue "B ARG 92": "NH1" <-> "NH2" Residue "B ARG 95": "NH1" <-> "NH2" Residue "C ARG 63": "NH1" <-> "NH2" Residue "C ARG 128": "NH1" <-> "NH2" Residue "D ARG 40": "NH1" <-> "NH2" Residue "D ARG 45": "NH1" <-> "NH2" Residue "D ARG 67": "NH1" <-> "NH2" Residue "E ARG 63": "NH1" <-> "NH2" Residue "E PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 134": "NH1" <-> "NH2" Residue "F ARG 92": "NH1" <-> "NH2" Residue "G ARG 63": "NH1" <-> "NH2" Residue "G ARG 69": "NH1" <-> "NH2" Residue "G GLU 94": "OE1" <-> "OE2" Residue "G GLU 105": "OE1" <-> "OE2" Residue "G ARG 131": "NH1" <-> "NH2" Residue "G ARG 134": "NH1" <-> "NH2" Residue "H ARG 36": "NH1" <-> "NH2" Residue "H GLU 52": "OE1" <-> "OE2" Residue "H ARG 95": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 9767 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 619 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 2, 'TRANS': 73} Chain: "B" Number of atoms: 587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 587 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 1, 'TRANS': 71} Chain: "C" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 625 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "D" Number of atoms: 568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 568 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 1, 'TRANS': 69} Chain: "E" Number of atoms: 619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 619 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 2, 'TRANS': 73} Chain: "F" Number of atoms: 576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 576 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 1, 'TRANS': 70} Chain: "G" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 625 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "H" Number of atoms: 587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 587 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 1, 'TRANS': 71} Chain: "I" Number of atoms: 2463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 2463 Classifications: {'DNA': 121} Link IDs: {'rna3p': 120} Chain: "J" Number of atoms: 2498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 2498 Classifications: {'DNA': 121} Link IDs: {'rna3p': 120} Time building chain proxies: 5.40, per 1000 atoms: 0.55 Number of scatterers: 9767 At special positions: 0 Unit cell: (120.75, 93.45, 111.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 20 16.00 P 242 15.00 O 2287 8.00 N 1845 7.00 C 5373 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 - 3.50 Amino acid : False - 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: 5.35 Conformation dependent library (CDL) restraints added in 916.6 milliseconds 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1126 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 6 sheets defined 78.8% alpha, 2.0% beta 120 base pairs and 187 stacking pairs defined. Time for finding SS restraints: 4.52 Creating SS restraints... Processing helix chain 'A' and resid 63 through 79 removed outlier: 3.798A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N PHE A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 131 Processing helix chain 'B' and resid 24 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'C' and resid 63 through 79 removed outlier: 3.517A pdb=" N PHE C 67 " --> pdb=" O ARG C 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 114 Processing helix chain 'C' and resid 120 through 132 Processing helix chain 'D' and resid 25 through 29 removed outlier: 3.559A pdb=" N ILE D 29 " --> pdb=" O ILE D 26 " (cutoff:3.500A) Processing helix chain 'D' and resid 30 through 41 Processing helix chain 'D' and resid 49 through 76 Processing helix chain 'D' and resid 82 through 93 Processing helix chain 'E' and resid 63 through 79 removed outlier: 3.720A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N PHE E 78 " --> pdb=" O ILE E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 Processing helix chain 'F' and resid 82 through 94 Processing helix chain 'G' and resid 63 through 79 removed outlier: 3.527A pdb=" N PHE G 67 " --> pdb=" O ARG G 63 " (cutoff:3.500A) Processing helix chain 'G' and resid 85 through 114 Processing helix chain 'G' and resid 120 through 131 Processing helix chain 'H' and resid 24 through 29 Processing helix chain 'H' and resid 30 through 41 Processing helix chain 'H' and resid 49 through 76 Processing helix chain 'H' and resid 82 through 93 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.862A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'C' and resid 118 through 119 Processing sheet with id=AA4, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA5, first strand: chain 'G' and resid 83 through 84 removed outlier: 6.812A pdb=" N ARG G 83 " --> pdb=" O VAL H 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'G' and resid 118 through 119 358 hydrogen bonds defined for protein. 1047 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 312 hydrogen bonds 624 hydrogen bond angles 0 basepair planarities 120 basepair parallelities 187 stacking parallelities Total time for adding SS restraints: 3.42 Time building geometry restraints manager: 5.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 1875 1.33 - 1.45: 3371 1.45 - 1.57: 4658 1.57 - 1.69: 482 1.69 - 1.81: 32 Bond restraints: 10418 Sorted by residual: bond pdb=" C3' DT I 14 " pdb=" O3' DT I 14 " ideal model delta sigma weight residual 1.422 1.467 -0.045 3.00e-02 1.11e+03 2.25e+00 bond pdb=" C3' DC I -48 " pdb=" O3' DC I -48 " ideal model delta sigma weight residual 1.422 1.466 -0.044 3.00e-02 1.11e+03 2.17e+00 bond pdb=" C3' DC I 51 " pdb=" O3' DC I 51 " ideal model delta sigma weight residual 1.422 1.458 -0.036 3.00e-02 1.11e+03 1.46e+00 bond pdb=" CG LYS H 77 " pdb=" CD LYS H 77 " ideal model delta sigma weight residual 1.520 1.485 0.035 3.00e-02 1.11e+03 1.34e+00 bond pdb=" CB MET B 84 " pdb=" CG MET B 84 " ideal model delta sigma weight residual 1.520 1.485 0.035 3.00e-02 1.11e+03 1.34e+00 ... (remaining 10413 not shown) Histogram of bond angle deviations from ideal: 98.28 - 105.13: 1006 105.13 - 111.98: 5732 111.98 - 118.83: 2674 118.83 - 125.68: 4880 125.68 - 132.53: 794 Bond angle restraints: 15086 Sorted by residual: angle pdb=" CB MET B 84 " pdb=" CG MET B 84 " pdb=" SD MET B 84 " ideal model delta sigma weight residual 112.70 104.00 8.70 3.00e+00 1.11e-01 8.41e+00 angle pdb=" CA ARG H 92 " pdb=" CB ARG H 92 " pdb=" CG ARG H 92 " ideal model delta sigma weight residual 114.10 119.61 -5.51 2.00e+00 2.50e-01 7.59e+00 angle pdb=" C ALA F 76 " pdb=" N LYS F 77 " pdb=" CA LYS F 77 " ideal model delta sigma weight residual 121.54 126.72 -5.18 1.91e+00 2.74e-01 7.35e+00 angle pdb=" C TYR D 51 " pdb=" N GLU D 52 " pdb=" CA GLU D 52 " ideal model delta sigma weight residual 120.28 116.66 3.62 1.34e+00 5.57e-01 7.31e+00 angle pdb=" N GLY D 56 " pdb=" CA GLY D 56 " pdb=" C GLY D 56 " ideal model delta sigma weight residual 112.50 109.51 2.99 1.16e+00 7.43e-01 6.62e+00 ... (remaining 15081 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.68: 4448 34.68 - 69.35: 1165 69.35 - 104.02: 32 104.02 - 138.70: 1 138.70 - 173.37: 3 Dihedral angle restraints: 5649 sinusoidal: 3920 harmonic: 1729 Sorted by residual: dihedral pdb=" C4' DC I 51 " pdb=" C3' DC I 51 " pdb=" O3' DC I 51 " pdb=" P DA I 52 " ideal model delta sinusoidal sigma weight residual 220.00 46.63 173.37 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" C4' DC I -48 " pdb=" C3' DC I -48 " pdb=" O3' DC I -48 " pdb=" P DG I -47 " ideal model delta sinusoidal sigma weight residual 220.00 49.06 170.94 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" C4' DT I 14 " pdb=" C3' DT I 14 " pdb=" O3' DT I 14 " pdb=" P DT I 15 " ideal model delta sinusoidal sigma weight residual 220.00 50.32 169.68 1 3.50e+01 8.16e-04 1.55e+01 ... (remaining 5646 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1330 0.036 - 0.072: 300 0.072 - 0.108: 78 0.108 - 0.143: 14 0.143 - 0.179: 1 Chirality restraints: 1723 Sorted by residual: chirality pdb=" CB VAL H 70 " pdb=" CA VAL H 70 " pdb=" CG1 VAL H 70 " pdb=" CG2 VAL H 70 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 8.03e-01 chirality pdb=" CA LYS H 77 " pdb=" N LYS H 77 " pdb=" C LYS H 77 " pdb=" CB LYS H 77 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.13e-01 chirality pdb=" CB ILE F 50 " pdb=" CA ILE F 50 " pdb=" CG1 ILE F 50 " pdb=" CG2 ILE F 50 " both_signs ideal model delta sigma weight residual False 2.64 2.79 -0.14 2.00e-01 2.50e+01 5.09e-01 ... (remaining 1720 not shown) Planarity restraints: 1072 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG B 67 " -0.021 2.00e-02 2.50e+03 4.20e-02 1.77e+01 pdb=" C ARG B 67 " 0.073 2.00e-02 2.50e+03 pdb=" O ARG B 67 " -0.027 2.00e-02 2.50e+03 pdb=" N ASP B 68 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU D 49 " 0.019 2.00e-02 2.50e+03 3.88e-02 1.50e+01 pdb=" C LEU D 49 " -0.067 2.00e-02 2.50e+03 pdb=" O LEU D 49 " 0.025 2.00e-02 2.50e+03 pdb=" N ILE D 50 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG D 67 " 0.019 2.00e-02 2.50e+03 3.83e-02 1.47e+01 pdb=" C ARG D 67 " -0.066 2.00e-02 2.50e+03 pdb=" O ARG D 67 " 0.025 2.00e-02 2.50e+03 pdb=" N ASP D 68 " 0.022 2.00e-02 2.50e+03 ... (remaining 1069 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 2199 2.81 - 3.33: 9187 3.33 - 3.85: 19761 3.85 - 4.38: 21986 4.38 - 4.90: 30534 Nonbonded interactions: 83667 Sorted by model distance: nonbonded pdb=" NE2 GLN A 125 " pdb=" OE2 GLU B 53 " model vdw 2.286 2.520 nonbonded pdb=" NH1 ARG F 35 " pdb=" OP2 DC I 39 " model vdw 2.322 2.520 nonbonded pdb=" OD2 ASP E 106 " pdb=" NH1 ARG E 131 " model vdw 2.337 2.520 nonbonded pdb=" NH1 ARG B 78 " pdb=" OP2 DC I -2 " model vdw 2.369 2.520 nonbonded pdb=" N SER A 86 " pdb=" OP1 DT J 7 " model vdw 2.375 2.520 ... (remaining 83662 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'C' and resid 59 through 134) selection = chain 'E' selection = (chain 'G' and resid 59 through 134) } ncs_group { reference = (chain 'B' and resid 25 through 94) selection = (chain 'D' and resid 25 through 94) selection = (chain 'F' and resid 25 through 94) selection = (chain 'H' and resid 25 through 94) } 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 group one per residue 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: 0.260 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: 1.670 Check model and map are aligned: 0.170 Set scattering table: 0.080 Process input model: 33.550 Find NCS groups from input model: 0.400 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:2.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7333 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 : 0.003 0.045 10418 Z= 0.196 Angle : 0.633 8.819 15086 Z= 0.411 Chirality : 0.034 0.179 1723 Planarity : 0.007 0.061 1072 Dihedral : 28.743 173.373 4523 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 0.20 % Allowed : 3.56 % Favored : 96.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.39 (0.29), residues: 579 helix: 0.79 (0.21), residues: 459 sheet: None (None), residues: 0 loop : -1.62 (0.38), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS H 75 PHE 0.016 0.001 PHE C 84 TYR 0.017 0.001 TYR B 88 ARG 0.011 0.000 ARG F 78 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 176 time to evaluate : 0.736 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 86 SER cc_start: 0.8582 (t) cc_final: 0.8232 (m) REVERT: E 64 LYS cc_start: 0.8483 (tptt) cc_final: 0.8135 (tptm) REVERT: F 55 ARG cc_start: 0.8091 (mtt90) cc_final: 0.7792 (mtt180) REVERT: G 86 SER cc_start: 0.8605 (t) cc_final: 0.8132 (p) outliers start: 1 outliers final: 0 residues processed: 176 average time/residue: 0.3794 time to fit residues: 80.9480 Evaluate side-chains 118 residues out of total 505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 118 time to evaluate : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 67 optimal weight: 10.0000 chunk 60 optimal weight: 10.0000 chunk 33 optimal weight: 4.9990 chunk 20 optimal weight: 5.9990 chunk 40 optimal weight: 20.0000 chunk 32 optimal weight: 0.6980 chunk 62 optimal weight: 10.0000 chunk 24 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 chunk 46 optimal weight: 0.6980 chunk 72 optimal weight: 10.0000 overall best weight: 2.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 HIS E 93 GLN E 125 GLN G 93 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.2456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 10418 Z= 0.320 Angle : 0.646 6.999 15086 Z= 0.371 Chirality : 0.035 0.133 1723 Planarity : 0.004 0.040 1072 Dihedral : 32.293 171.974 3289 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 4.75 % Allowed : 13.47 % Favored : 81.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 1.81 (0.33), residues: 579 helix: 1.92 (0.24), residues: 459 sheet: None (None), residues: 0 loop : -1.67 (0.38), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS H 75 PHE 0.013 0.002 PHE A 78 TYR 0.010 0.002 TYR A 99 ARG 0.006 0.001 ARG H 92 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 141 time to evaluate : 0.658 Fit side-chains revert: symmetry clash REVERT: A 86 SER cc_start: 0.8420 (t) cc_final: 0.8063 (p) REVERT: A 87 SER cc_start: 0.9062 (m) cc_final: 0.8772 (p) REVERT: G 86 SER cc_start: 0.8681 (t) cc_final: 0.8270 (p) REVERT: G 112 ILE cc_start: 0.9122 (tp) cc_final: 0.8802 (tp) outliers start: 24 outliers final: 17 residues processed: 152 average time/residue: 0.2847 time to fit residues: 56.2623 Evaluate side-chains 137 residues out of total 505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 120 time to evaluate : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 49 LEU Chi-restraints excluded: chain H residue 54 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 40 optimal weight: 10.0000 chunk 22 optimal weight: 3.9990 chunk 60 optimal weight: 10.0000 chunk 49 optimal weight: 1.9990 chunk 20 optimal weight: 8.9990 chunk 72 optimal weight: 9.9990 chunk 78 optimal weight: 10.0000 chunk 64 optimal weight: 10.0000 chunk 24 optimal weight: 0.9990 chunk 58 optimal weight: 8.9990 chunk 71 optimal weight: 6.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 125 GLN F 25 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.4159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.073 10418 Z= 0.482 Angle : 0.737 7.369 15086 Z= 0.419 Chirality : 0.040 0.160 1723 Planarity : 0.005 0.038 1072 Dihedral : 33.115 177.921 3289 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 14.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 5.94 % Allowed : 17.62 % Favored : 76.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 1.53 (0.33), residues: 579 helix: 1.82 (0.24), residues: 453 sheet: None (None), residues: 0 loop : -2.10 (0.41), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 113 PHE 0.022 0.003 PHE C 67 TYR 0.016 0.002 TYR A 99 ARG 0.008 0.001 ARG H 92 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 127 time to evaluate : 0.726 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 86 SER cc_start: 0.8697 (t) cc_final: 0.8141 (p) REVERT: A 87 SER cc_start: 0.9151 (m) cc_final: 0.8794 (t) REVERT: A 125 GLN cc_start: 0.7384 (OUTLIER) cc_final: 0.7102 (mp10) REVERT: E 116 ARG cc_start: 0.8471 (OUTLIER) cc_final: 0.7760 (mtm-85) REVERT: G 73 GLU cc_start: 0.8572 (tm-30) cc_final: 0.8354 (tt0) REVERT: G 86 SER cc_start: 0.8786 (t) cc_final: 0.8292 (p) REVERT: H 79 LYS cc_start: 0.8659 (mttt) cc_final: 0.8391 (mttp) outliers start: 30 outliers final: 22 residues processed: 148 average time/residue: 0.2880 time to fit residues: 55.0299 Evaluate side-chains 135 residues out of total 505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 111 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 75 HIS Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 116 ARG Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 49 LEU Chi-restraints excluded: chain H residue 54 THR Chi-restraints excluded: chain H residue 84 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 54 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 48 optimal weight: 0.8980 chunk 73 optimal weight: 10.0000 chunk 77 optimal weight: 8.9990 chunk 38 optimal weight: 0.9980 chunk 69 optimal weight: 10.0000 chunk 20 optimal weight: 1.9990 chunk 64 optimal weight: 10.0000 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN C 68 GLN D 25 ASN E 125 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.3936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10418 Z= 0.221 Angle : 0.605 7.998 15086 Z= 0.352 Chirality : 0.033 0.145 1723 Planarity : 0.004 0.032 1072 Dihedral : 32.682 179.119 3289 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 4.36 % Allowed : 21.58 % Favored : 74.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 2.32 (0.34), residues: 579 helix: 2.35 (0.23), residues: 457 sheet: None (None), residues: 0 loop : -1.79 (0.41), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 75 PHE 0.013 0.002 PHE E 67 TYR 0.010 0.001 TYR B 88 ARG 0.006 0.000 ARG F 78 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 122 time to evaluate : 0.707 Fit side-chains REVERT: A 86 SER cc_start: 0.8572 (t) cc_final: 0.8107 (p) REVERT: B 84 MET cc_start: 0.7475 (tpp) cc_final: 0.7212 (tpp) REVERT: E 93 GLN cc_start: 0.7858 (tt0) cc_final: 0.7615 (tt0) REVERT: F 78 ARG cc_start: 0.6499 (mtm-85) cc_final: 0.6237 (mtm180) REVERT: G 86 SER cc_start: 0.8623 (t) cc_final: 0.8219 (p) REVERT: H 79 LYS cc_start: 0.8597 (mttt) cc_final: 0.8326 (mttp) outliers start: 22 outliers final: 13 residues processed: 137 average time/residue: 0.2926 time to fit residues: 51.6519 Evaluate side-chains 122 residues out of total 505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 109 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 75 HIS Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain G residue 80 THR Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 49 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 43 optimal weight: 1.9990 chunk 1 optimal weight: 5.9990 chunk 57 optimal weight: 10.0000 chunk 31 optimal weight: 1.9990 chunk 65 optimal weight: 10.0000 chunk 53 optimal weight: 0.7980 chunk 0 optimal weight: 3.9990 chunk 39 optimal weight: 0.9980 chunk 69 optimal weight: 10.0000 chunk 19 optimal weight: 0.6980 chunk 26 optimal weight: 9.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 68 GLN D 25 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.3928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10418 Z= 0.222 Angle : 0.596 7.981 15086 Z= 0.347 Chirality : 0.034 0.165 1723 Planarity : 0.004 0.030 1072 Dihedral : 32.572 178.385 3289 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 3.96 % Allowed : 23.76 % Favored : 72.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 2.60 (0.34), residues: 579 helix: 2.52 (0.23), residues: 457 sheet: None (None), residues: 0 loop : -1.53 (0.44), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 75 PHE 0.015 0.002 PHE C 67 TYR 0.011 0.001 TYR B 88 ARG 0.006 0.000 ARG B 40 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 121 time to evaluate : 0.748 Fit side-chains revert: symmetry clash REVERT: A 86 SER cc_start: 0.8466 (t) cc_final: 0.8001 (p) REVERT: G 86 SER cc_start: 0.8551 (t) cc_final: 0.8171 (p) outliers start: 20 outliers final: 13 residues processed: 133 average time/residue: 0.2878 time to fit residues: 49.6025 Evaluate side-chains 121 residues out of total 505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 108 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain D residue 25 ASN Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 75 HIS Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain G residue 80 THR Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 49 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 69 optimal weight: 10.0000 chunk 15 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 19 optimal weight: 0.5980 chunk 77 optimal weight: 10.0000 chunk 64 optimal weight: 10.0000 chunk 35 optimal weight: 8.9990 chunk 6 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 40 optimal weight: 6.9990 chunk 74 optimal weight: 8.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 68 GLN D 25 ASN E 125 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.3983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10418 Z= 0.219 Angle : 0.606 9.062 15086 Z= 0.348 Chirality : 0.033 0.144 1723 Planarity : 0.004 0.040 1072 Dihedral : 32.496 177.268 3289 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 4.55 % Allowed : 24.55 % Favored : 70.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 2.75 (0.34), residues: 579 helix: 2.65 (0.24), residues: 451 sheet: None (None), residues: 0 loop : -1.41 (0.43), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 75 PHE 0.012 0.001 PHE E 67 TYR 0.009 0.001 TYR H 72 ARG 0.007 0.000 ARG H 92 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 109 time to evaluate : 0.703 Fit side-chains REVERT: A 86 SER cc_start: 0.8433 (t) cc_final: 0.7975 (p) REVERT: B 84 MET cc_start: 0.7402 (tpp) cc_final: 0.7122 (tpp) REVERT: G 86 SER cc_start: 0.8516 (t) cc_final: 0.8141 (p) outliers start: 23 outliers final: 17 residues processed: 124 average time/residue: 0.2503 time to fit residues: 41.4107 Evaluate side-chains 122 residues out of total 505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 105 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain D residue 25 ASN Chi-restraints excluded: chain D residue 26 ILE Chi-restraints excluded: chain D residue 75 HIS Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain G residue 80 THR Chi-restraints excluded: chain G residue 124 ILE Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 49 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 8 optimal weight: 0.9980 chunk 44 optimal weight: 6.9990 chunk 56 optimal weight: 20.0000 chunk 43 optimal weight: 0.7980 chunk 65 optimal weight: 10.0000 chunk 77 optimal weight: 10.0000 chunk 48 optimal weight: 0.7980 chunk 47 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 chunk 30 optimal weight: 9.9990 chunk 46 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 68 GLN D 25 ASN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 125 GLN F 64 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.3994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10418 Z= 0.192 Angle : 0.587 9.180 15086 Z= 0.340 Chirality : 0.033 0.142 1723 Planarity : 0.003 0.031 1072 Dihedral : 32.338 175.524 3289 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 3.56 % Allowed : 26.93 % Favored : 69.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 2.80 (0.34), residues: 579 helix: 2.65 (0.23), residues: 457 sheet: None (None), residues: 0 loop : -1.45 (0.44), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 75 PHE 0.012 0.001 PHE C 67 TYR 0.010 0.001 TYR H 72 ARG 0.006 0.000 ARG H 92 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 107 time to evaluate : 0.787 Fit side-chains REVERT: A 86 SER cc_start: 0.8340 (t) cc_final: 0.7960 (p) REVERT: B 84 MET cc_start: 0.7444 (tpp) cc_final: 0.7202 (tpp) REVERT: F 44 LYS cc_start: 0.8732 (mmpt) cc_final: 0.8329 (mmtm) REVERT: G 86 SER cc_start: 0.8377 (t) cc_final: 0.8045 (p) REVERT: H 84 MET cc_start: 0.7574 (tpp) cc_final: 0.7071 (tpp) outliers start: 18 outliers final: 12 residues processed: 120 average time/residue: 0.2645 time to fit residues: 42.1084 Evaluate side-chains 110 residues out of total 505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 98 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain D residue 26 ILE Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 75 HIS Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain G residue 80 THR Chi-restraints excluded: chain G residue 124 ILE Chi-restraints excluded: chain H residue 30 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 23 optimal weight: 0.2980 chunk 15 optimal weight: 3.9990 chunk 14 optimal weight: 8.9990 chunk 49 optimal weight: 0.6980 chunk 52 optimal weight: 0.6980 chunk 38 optimal weight: 0.7980 chunk 7 optimal weight: 5.9990 chunk 60 optimal weight: 10.0000 chunk 70 optimal weight: 10.0000 chunk 73 optimal weight: 10.0000 chunk 67 optimal weight: 10.0000 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 68 GLN E 125 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.4109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10418 Z= 0.217 Angle : 0.601 9.298 15086 Z= 0.345 Chirality : 0.033 0.139 1723 Planarity : 0.003 0.034 1072 Dihedral : 32.354 174.616 3289 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 3.56 % Allowed : 27.52 % Favored : 68.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.75 (0.34), residues: 579 helix: 2.64 (0.24), residues: 457 sheet: None (None), residues: 0 loop : -1.55 (0.44), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 75 PHE 0.018 0.002 PHE E 67 TYR 0.009 0.001 TYR B 88 ARG 0.006 0.000 ARG H 92 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 104 time to evaluate : 0.730 Fit side-chains REVERT: A 86 SER cc_start: 0.8369 (t) cc_final: 0.7962 (p) REVERT: G 86 SER cc_start: 0.8404 (t) cc_final: 0.8066 (p) REVERT: G 112 ILE cc_start: 0.9013 (tp) cc_final: 0.8748 (tp) outliers start: 18 outliers final: 16 residues processed: 117 average time/residue: 0.2621 time to fit residues: 41.1071 Evaluate side-chains 118 residues out of total 505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 102 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain D residue 29 ILE Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 75 HIS Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain G residue 80 THR Chi-restraints excluded: chain G residue 124 ILE Chi-restraints excluded: chain H residue 30 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 71 optimal weight: 7.9990 chunk 73 optimal weight: 10.0000 chunk 43 optimal weight: 0.9990 chunk 31 optimal weight: 3.9990 chunk 56 optimal weight: 20.0000 chunk 22 optimal weight: 1.9990 chunk 64 optimal weight: 10.0000 chunk 67 optimal weight: 10.0000 chunk 47 optimal weight: 0.8980 chunk 75 optimal weight: 10.0000 chunk 46 optimal weight: 0.8980 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 68 GLN E 125 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.4282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10418 Z= 0.250 Angle : 0.629 11.504 15086 Z= 0.356 Chirality : 0.034 0.141 1723 Planarity : 0.004 0.032 1072 Dihedral : 32.419 174.429 3289 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 13.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 3.76 % Allowed : 28.32 % Favored : 67.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 2.60 (0.34), residues: 579 helix: 2.55 (0.24), residues: 457 sheet: None (None), residues: 0 loop : -1.67 (0.44), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 75 PHE 0.020 0.002 PHE E 67 TYR 0.006 0.001 TYR B 51 ARG 0.005 0.000 ARG H 92 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 108 time to evaluate : 0.790 Fit side-chains REVERT: A 86 SER cc_start: 0.8454 (t) cc_final: 0.7958 (p) REVERT: B 84 MET cc_start: 0.7539 (tpp) cc_final: 0.6921 (tpp) REVERT: C 82 LEU cc_start: 0.7837 (mm) cc_final: 0.7361 (mt) REVERT: F 84 MET cc_start: 0.7204 (tpp) cc_final: 0.6993 (tpp) REVERT: G 76 GLN cc_start: 0.7634 (pp30) cc_final: 0.7409 (pp30) REVERT: G 86 SER cc_start: 0.8501 (t) cc_final: 0.8104 (p) REVERT: G 112 ILE cc_start: 0.9033 (tp) cc_final: 0.8777 (tp) REVERT: H 84 MET cc_start: 0.7615 (tpp) cc_final: 0.7145 (tpp) outliers start: 19 outliers final: 15 residues processed: 122 average time/residue: 0.2580 time to fit residues: 42.1510 Evaluate side-chains 120 residues out of total 505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 105 time to evaluate : 0.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain D residue 29 ILE Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 75 HIS Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain G residue 80 THR Chi-restraints excluded: chain G residue 124 ILE Chi-restraints excluded: chain H residue 30 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 36 optimal weight: 1.9990 chunk 52 optimal weight: 0.6980 chunk 79 optimal weight: 10.0000 chunk 73 optimal weight: 10.0000 chunk 63 optimal weight: 10.0000 chunk 6 optimal weight: 0.5980 chunk 49 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 chunk 50 optimal weight: 0.0770 chunk 67 optimal weight: 10.0000 chunk 19 optimal weight: 0.8980 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 68 GLN E 125 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.4289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10418 Z= 0.193 Angle : 0.618 11.168 15086 Z= 0.349 Chirality : 0.033 0.147 1723 Planarity : 0.003 0.032 1072 Dihedral : 32.148 173.570 3289 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 3.17 % Allowed : 28.91 % Favored : 67.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 2.80 (0.34), residues: 579 helix: 2.66 (0.24), residues: 457 sheet: None (None), residues: 0 loop : -1.47 (0.44), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS F 75 PHE 0.014 0.001 PHE E 67 TYR 0.011 0.001 TYR H 72 ARG 0.005 0.000 ARG H 92 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 106 time to evaluate : 0.803 Fit side-chains REVERT: A 86 SER cc_start: 0.8313 (t) cc_final: 0.7936 (p) REVERT: C 82 LEU cc_start: 0.7890 (mm) cc_final: 0.7486 (mt) REVERT: F 44 LYS cc_start: 0.8791 (mmpt) cc_final: 0.8322 (mmtm) REVERT: G 86 SER cc_start: 0.8356 (t) cc_final: 0.8000 (p) REVERT: H 84 MET cc_start: 0.7525 (tpp) cc_final: 0.7098 (tpp) outliers start: 16 outliers final: 12 residues processed: 117 average time/residue: 0.2568 time to fit residues: 40.2594 Evaluate side-chains 101 residues out of total 505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 89 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain C residue 76 GLN Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain D residue 29 ILE Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain G residue 80 THR Chi-restraints excluded: chain G residue 124 ILE Chi-restraints excluded: chain H residue 30 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 58 optimal weight: 10.0000 chunk 9 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 63 optimal weight: 10.0000 chunk 26 optimal weight: 0.8980 chunk 65 optimal weight: 10.0000 chunk 8 optimal weight: 0.9980 chunk 11 optimal weight: 0.8980 chunk 55 optimal weight: 0.6980 chunk 3 optimal weight: 0.9980 chunk 45 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 68 GLN F 25 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4507 r_free = 0.4507 target = 0.165539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.125999 restraints weight = 19619.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.128257 restraints weight = 14422.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.128793 restraints weight = 14713.014| |-----------------------------------------------------------------------------| r_work (final): 0.3968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.4307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 10418 Z= 0.204 Angle : 0.611 10.938 15086 Z= 0.348 Chirality : 0.033 0.156 1723 Planarity : 0.004 0.047 1072 Dihedral : 32.148 174.373 3289 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.57 % Allowed : 30.10 % Favored : 67.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 2.83 (0.34), residues: 579 helix: 2.71 (0.24), residues: 457 sheet: None (None), residues: 0 loop : -1.58 (0.44), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 75 PHE 0.019 0.001 PHE E 67 TYR 0.011 0.001 TYR H 72 ARG 0.009 0.000 ARG H 92 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1677.75 seconds wall clock time: 31 minutes 17.11 seconds (1877.11 seconds total)