Starting phenix.real_space_refine on Thu Mar 14 08:11:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zhy_11221/03_2024/6zhy_11221.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zhy_11221/03_2024/6zhy_11221.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zhy_11221/03_2024/6zhy_11221.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zhy_11221/03_2024/6zhy_11221.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zhy_11221/03_2024/6zhy_11221.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zhy_11221/03_2024/6zhy_11221.pdb" } resolution = 3.0 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= 0.002 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 218 5.49 5 S 8 5.16 5 C 4968 2.51 5 N 1700 2.21 5 O 2105 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 8999 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 801 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "B" Number of atoms: 673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 673 Classifications: {'peptide': 84} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 82} Chain: "C" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 813 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "D" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 745 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "E" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 807 Classifications: {'peptide': 98} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 94} Chain: "F" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 627 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "I" Number of atoms: 2236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 2236 Classifications: {'DNA': 110} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 109} Chain: "J" Number of atoms: 2268 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 2268 Classifications: {'DNA': 110} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 109} Chain: "K" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 29 Classifications: {'peptide': 4} Link IDs: {'TRANS': 3} Time building chain proxies: 5.11, per 1000 atoms: 0.57 Number of scatterers: 8999 At special positions: 0 Unit cell: (115.758, 107.256, 101.37, 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 8 16.00 P 218 15.00 O 2105 8.00 N 1700 7.00 C 4968 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: 5.08 Conformation dependent library (CDL) restraints added in 1.0 seconds 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1052 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 7 sheets defined 73.5% alpha, 2.5% beta 110 base pairs and 196 stacking pairs defined. Time for finding SS restraints: 5.36 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 removed outlier: 4.097A pdb=" N LEU A 48 " --> pdb=" O GLY A 44 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ARG A 49 " --> pdb=" O THR A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 79 removed outlier: 3.860A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 3.853A 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 132 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 removed outlier: 3.787A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.400A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 89 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 52 through 81 Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 100 through 121 removed outlier: 3.588A pdb=" N LYS D 105 " --> pdb=" O GLY D 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 79 removed outlier: 3.818A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) removed outlier: 3.915A 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 131 Processing helix chain 'F' and resid 24 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 93 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.663A 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 42 through 43 removed outlier: 7.157A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA5, first strand: chain 'C' and resid 101 through 102 removed outlier: 6.620A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.472A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 118 through 119 306 hydrogen bonds defined for protein. 894 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 285 hydrogen bonds 570 hydrogen bond angles 0 basepair planarities 110 basepair parallelities 196 stacking parallelities Total time for adding SS restraints: 4.18 Time building geometry restraints manager: 5.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1561 1.33 - 1.45: 3291 1.45 - 1.57: 4300 1.57 - 1.69: 437 1.69 - 1.81: 16 Bond restraints: 9605 Sorted by residual: bond pdb=" C3' DC I 6 " pdb=" C2' DC I 6 " ideal model delta sigma weight residual 1.525 1.562 -0.037 2.00e-02 2.50e+03 3.43e+00 bond pdb=" C3' DT J 69 " pdb=" C2' DT J 69 " ideal model delta sigma weight residual 1.525 1.561 -0.036 2.00e-02 2.50e+03 3.29e+00 bond pdb=" C3' DC I 4 " pdb=" C2' DC I 4 " ideal model delta sigma weight residual 1.525 1.561 -0.036 2.00e-02 2.50e+03 3.27e+00 bond pdb=" CB PRO A 38 " pdb=" CG PRO A 38 " ideal model delta sigma weight residual 1.492 1.574 -0.082 5.00e-02 4.00e+02 2.67e+00 bond pdb=" C3' DG J -19 " pdb=" C2' DG J -19 " ideal model delta sigma weight residual 1.525 1.557 -0.032 2.00e-02 2.50e+03 2.63e+00 ... (remaining 9600 not shown) Histogram of bond angle deviations from ideal: 98.00 - 104.97: 878 104.97 - 111.94: 4991 111.94 - 118.90: 2852 118.90 - 125.87: 4498 125.87 - 132.84: 688 Bond angle restraints: 13907 Sorted by residual: angle pdb=" O3' DT J -17 " pdb=" C3' DT J -17 " pdb=" C2' DT J -17 " ideal model delta sigma weight residual 111.50 117.50 -6.00 1.50e+00 4.44e-01 1.60e+01 angle pdb=" C4' DT I 30 " pdb=" O4' DT I 30 " pdb=" C1' DT I 30 " ideal model delta sigma weight residual 109.70 103.81 5.89 1.50e+00 4.44e-01 1.54e+01 angle pdb=" C3' DG J 20 " pdb=" O3' DG J 20 " pdb=" P DG J 21 " ideal model delta sigma weight residual 120.20 125.97 -5.77 1.50e+00 4.44e-01 1.48e+01 angle pdb=" O4' DG I 26 " pdb=" C1' DG I 26 " pdb=" N9 DG I 26 " ideal model delta sigma weight residual 108.40 102.78 5.62 1.50e+00 4.44e-01 1.41e+01 angle pdb=" O4' DG I 28 " pdb=" C1' DG I 28 " pdb=" N9 DG I 28 " ideal model delta sigma weight residual 108.40 102.99 5.41 1.50e+00 4.44e-01 1.30e+01 ... (remaining 13902 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.42: 4197 33.42 - 66.83: 967 66.83 - 100.25: 36 100.25 - 133.66: 0 133.66 - 167.07: 2 Dihedral angle restraints: 5202 sinusoidal: 3573 harmonic: 1629 Sorted by residual: dihedral pdb=" CA PRO D 100 " pdb=" C PRO D 100 " pdb=" N GLY D 101 " pdb=" CA GLY D 101 " ideal model delta harmonic sigma weight residual 180.00 153.18 26.82 0 5.00e+00 4.00e-02 2.88e+01 dihedral pdb=" CA THR D 85 " pdb=" C THR D 85 " pdb=" N ILE D 86 " pdb=" CA ILE D 86 " ideal model delta harmonic sigma weight residual 180.00 157.65 22.35 0 5.00e+00 4.00e-02 2.00e+01 dihedral pdb=" CA PHE E 84 " pdb=" C PHE E 84 " pdb=" N GLN E 85 " pdb=" CA GLN E 85 " ideal model delta harmonic sigma weight residual 180.00 160.31 19.69 0 5.00e+00 4.00e-02 1.55e+01 ... (remaining 5199 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 1285 0.068 - 0.136: 245 0.136 - 0.204: 25 0.204 - 0.273: 18 0.273 - 0.341: 6 Chirality restraints: 1579 Sorted by residual: chirality pdb=" C4' DT J 69 " pdb=" C5' DT J 69 " pdb=" O4' DT J 69 " pdb=" C3' DT J 69 " both_signs ideal model delta sigma weight residual False -2.53 -2.18 -0.34 2.00e-01 2.50e+01 2.90e+00 chirality pdb=" C4' DC I 4 " pdb=" C5' DC I 4 " pdb=" O4' DC I 4 " pdb=" C3' DC I 4 " both_signs ideal model delta sigma weight residual False -2.53 -2.22 -0.30 2.00e-01 2.50e+01 2.29e+00 chirality pdb=" C3' DG J 20 " pdb=" C4' DG J 20 " pdb=" O3' DG J 20 " pdb=" C2' DG J 20 " both_signs ideal model delta sigma weight residual False -2.66 -2.37 -0.29 2.00e-01 2.50e+01 2.09e+00 ... (remaining 1576 not shown) Planarity restraints: 999 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DC I 6 " -0.063 2.00e-02 2.50e+03 3.45e-02 2.67e+01 pdb=" N1 DC I 6 " 0.075 2.00e-02 2.50e+03 pdb=" C2 DC I 6 " -0.016 2.00e-02 2.50e+03 pdb=" O2 DC I 6 " 0.018 2.00e-02 2.50e+03 pdb=" N3 DC I 6 " -0.003 2.00e-02 2.50e+03 pdb=" C4 DC I 6 " -0.007 2.00e-02 2.50e+03 pdb=" N4 DC I 6 " -0.020 2.00e-02 2.50e+03 pdb=" C5 DC I 6 " 0.008 2.00e-02 2.50e+03 pdb=" C6 DC I 6 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC I 4 " -0.053 2.00e-02 2.50e+03 3.09e-02 2.14e+01 pdb=" N1 DC I 4 " 0.071 2.00e-02 2.50e+03 pdb=" C2 DC I 4 " -0.017 2.00e-02 2.50e+03 pdb=" O2 DC I 4 " 0.013 2.00e-02 2.50e+03 pdb=" N3 DC I 4 " -0.001 2.00e-02 2.50e+03 pdb=" C4 DC I 4 " -0.005 2.00e-02 2.50e+03 pdb=" N4 DC I 4 " -0.014 2.00e-02 2.50e+03 pdb=" C5 DC I 4 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DC I 4 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC J 19 " -0.042 2.00e-02 2.50e+03 2.86e-02 1.84e+01 pdb=" N1 DC J 19 " 0.069 2.00e-02 2.50e+03 pdb=" C2 DC J 19 " -0.025 2.00e-02 2.50e+03 pdb=" O2 DC J 19 " 0.010 2.00e-02 2.50e+03 pdb=" N3 DC J 19 " 0.002 2.00e-02 2.50e+03 pdb=" C4 DC J 19 " -0.003 2.00e-02 2.50e+03 pdb=" N4 DC J 19 " -0.007 2.00e-02 2.50e+03 pdb=" C5 DC J 19 " -0.006 2.00e-02 2.50e+03 pdb=" C6 DC J 19 " 0.002 2.00e-02 2.50e+03 ... (remaining 996 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.83: 2053 2.83 - 3.35: 8482 3.35 - 3.87: 18066 3.87 - 4.38: 21277 4.38 - 4.90: 29320 Nonbonded interactions: 79198 Sorted by model distance: nonbonded pdb=" OE1 GLN B 93 " pdb=" NH1 ARG B 95 " model vdw 2.316 2.520 nonbonded pdb=" NH2 ARG E 116 " pdb=" OD1 ASP E 123 " model vdw 2.376 2.520 nonbonded pdb=" OH TYR E 99 " pdb=" OE1 GLU E 133 " model vdw 2.406 2.440 nonbonded pdb=" OD2 ASP D 65 " pdb=" OH TYR F 98 " model vdw 2.420 2.440 nonbonded pdb=" OE1 GLU D 68 " pdb=" NZ LYS F 91 " model vdw 2.427 2.520 ... (remaining 79193 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 'E' and resid 38 through 134) } ncs_group { reference = (chain 'B' and resid 24 through 102) selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 5.820 Check model and map are aligned: 0.140 Set scattering table: 0.080 Process input model: 34.090 Find NCS groups from input model: 0.330 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:11.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 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 : 0.005 0.082 9605 Z= 0.248 Angle : 0.911 5.999 13907 Z= 0.590 Chirality : 0.061 0.341 1579 Planarity : 0.014 0.138 999 Dihedral : 27.253 167.075 4150 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 0.21 % Allowed : 0.43 % Favored : 99.36 % 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: 0.65 (0.31), residues: 548 helix: 0.73 (0.23), residues: 394 sheet: None (None), residues: 0 loop : -0.05 (0.44), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 75 PHE 0.010 0.001 PHE F 100 TYR 0.027 0.004 TYR C 57 ARG 0.030 0.004 ARG A 83 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 469 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 182 time to evaluate : 0.685 Fit side-chains revert: symmetry clash REVERT: B 74 GLU cc_start: 0.7978 (mt-10) cc_final: 0.7738 (mt-10) REVERT: C 90 ASP cc_start: 0.8348 (t70) cc_final: 0.8132 (t70) REVERT: F 31 LYS cc_start: 0.8916 (tttt) cc_final: 0.8648 (tttp) outliers start: 1 outliers final: 0 residues processed: 182 average time/residue: 102.7953 time to fit residues: 18722.3732 Evaluate side-chains 123 residues out of total 469 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 123 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 62 optimal weight: 10.0000 chunk 56 optimal weight: 7.9990 chunk 31 optimal weight: 6.9990 chunk 19 optimal weight: 5.9990 chunk 37 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 58 optimal weight: 7.9990 chunk 22 optimal weight: 0.9990 chunk 35 optimal weight: 5.9990 chunk 43 optimal weight: 0.6980 chunk 67 optimal weight: 6.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS A 68 GLN A 125 GLN C 73 ASN D 44 GLN D 46 HIS D 92 GLN E 39 HIS E 68 GLN E 85 GLN E 125 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.2533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 9605 Z= 0.270 Angle : 0.640 5.675 13907 Z= 0.390 Chirality : 0.038 0.141 1579 Planarity : 0.005 0.044 999 Dihedral : 31.953 165.895 3019 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Rotamer: Outliers : 4.26 % Allowed : 16.42 % Favored : 79.32 % 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 (0.35), residues: 548 helix: 2.48 (0.25), residues: 399 sheet: None (None), residues: 0 loop : 0.15 (0.47), residues: 149 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 31 PHE 0.009 0.001 PHE E 67 TYR 0.010 0.001 TYR C 57 ARG 0.009 0.001 ARG B 92 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 469 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 140 time to evaluate : 0.700 Fit side-chains revert: symmetry clash REVERT: B 53 GLU cc_start: 0.8417 (tp30) cc_final: 0.8090 (tp30) REVERT: B 74 GLU cc_start: 0.7987 (mt-10) cc_final: 0.7770 (mt-10) REVERT: F 31 LYS cc_start: 0.8979 (tttt) cc_final: 0.8727 (tttp) outliers start: 20 outliers final: 9 residues processed: 147 average time/residue: 1.4673 time to fit residues: 227.0921 Evaluate side-chains 137 residues out of total 469 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 128 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain C residue 72 ASP Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain F residue 73 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 37 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 chunk 55 optimal weight: 6.9990 chunk 45 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 67 optimal weight: 7.9990 chunk 72 optimal weight: 7.9990 chunk 59 optimal weight: 5.9990 chunk 66 optimal weight: 4.9990 chunk 22 optimal weight: 5.9990 chunk 54 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: A 68 GLN C 68 ASN D 44 GLN D 46 HIS E 68 GLN E 113 HIS E 125 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 moved from start: 0.2943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.048 9605 Z= 0.447 Angle : 0.657 5.670 13907 Z= 0.394 Chirality : 0.040 0.152 1579 Planarity : 0.005 0.043 999 Dihedral : 31.831 176.502 3019 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 6.61 % Allowed : 17.91 % Favored : 75.48 % 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: 2.76 (0.35), residues: 548 helix: 2.50 (0.25), residues: 402 sheet: None (None), residues: 0 loop : -0.07 (0.48), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS D 46 PHE 0.010 0.002 PHE D 67 TYR 0.011 0.002 TYR F 51 ARG 0.007 0.001 ARG D 83 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 469 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 121 time to evaluate : 0.696 Fit side-chains revert: symmetry clash REVERT: B 53 GLU cc_start: 0.8466 (tp30) cc_final: 0.8168 (tp30) REVERT: B 74 GLU cc_start: 0.8005 (mt-10) cc_final: 0.7783 (mt-10) REVERT: C 56 GLU cc_start: 0.8381 (OUTLIER) cc_final: 0.8084 (tt0) REVERT: F 31 LYS cc_start: 0.9008 (tttt) cc_final: 0.8772 (tttp) outliers start: 31 outliers final: 15 residues processed: 138 average time/residue: 1.5448 time to fit residues: 224.0182 Evaluate side-chains 136 residues out of total 469 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 120 time to evaluate : 0.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 93 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 66 optimal weight: 5.9990 chunk 50 optimal weight: 0.9980 chunk 34 optimal weight: 4.9990 chunk 7 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 67 optimal weight: 5.9990 chunk 71 optimal weight: 5.9990 chunk 35 optimal weight: 1.9990 chunk 64 optimal weight: 8.9990 chunk 19 optimal weight: 3.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN A 113 HIS E 68 GLN E 125 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.3153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 9605 Z= 0.252 Angle : 0.585 5.441 13907 Z= 0.356 Chirality : 0.035 0.134 1579 Planarity : 0.004 0.046 999 Dihedral : 31.459 179.486 3019 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 3.84 % Allowed : 20.47 % Favored : 75.69 % 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: 3.10 (0.36), residues: 548 helix: 2.79 (0.25), residues: 404 sheet: None (None), residues: 0 loop : -0.16 (0.48), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.000 HIS B 75 PHE 0.007 0.001 PHE E 67 TYR 0.008 0.001 TYR F 51 ARG 0.008 0.000 ARG D 83 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 469 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 131 time to evaluate : 0.705 Fit side-chains revert: symmetry clash REVERT: B 53 GLU cc_start: 0.8361 (tp30) cc_final: 0.8056 (tp30) REVERT: B 74 GLU cc_start: 0.7988 (mt-10) cc_final: 0.7723 (mt-10) outliers start: 18 outliers final: 11 residues processed: 138 average time/residue: 1.5294 time to fit residues: 221.8547 Evaluate side-chains 136 residues out of total 469 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 125 time to evaluate : 0.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 73 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 59 optimal weight: 5.9990 chunk 40 optimal weight: 3.9990 chunk 1 optimal weight: 0.8980 chunk 53 optimal weight: 7.9990 chunk 29 optimal weight: 0.8980 chunk 61 optimal weight: 8.9990 chunk 49 optimal weight: 3.9990 chunk 0 optimal weight: 30.0000 chunk 36 optimal weight: 6.9990 chunk 64 optimal weight: 6.9990 chunk 18 optimal weight: 5.9990 overall best weight: 3.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN E 68 GLN E 125 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.3343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 9605 Z= 0.332 Angle : 0.606 6.058 13907 Z= 0.363 Chirality : 0.036 0.135 1579 Planarity : 0.005 0.046 999 Dihedral : 31.476 175.756 3019 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 5.54 % Allowed : 20.26 % Favored : 74.20 % 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: 3.15 (0.36), residues: 548 helix: 2.80 (0.26), residues: 405 sheet: None (None), residues: 0 loop : -0.08 (0.50), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 75 PHE 0.008 0.001 PHE E 67 TYR 0.010 0.001 TYR F 51 ARG 0.010 0.000 ARG B 35 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 469 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 126 time to evaluate : 0.678 Fit side-chains revert: symmetry clash REVERT: B 53 GLU cc_start: 0.8390 (tp30) cc_final: 0.8116 (tp30) REVERT: B 74 GLU cc_start: 0.8013 (mt-10) cc_final: 0.7779 (mt-10) REVERT: E 129 ARG cc_start: 0.8611 (OUTLIER) cc_final: 0.8301 (tpt-90) outliers start: 26 outliers final: 18 residues processed: 138 average time/residue: 1.5433 time to fit residues: 223.7350 Evaluate side-chains 141 residues out of total 469 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 122 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain B residue 31 LYS Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 129 ARG Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 73 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 24 optimal weight: 4.9990 chunk 64 optimal weight: 8.9990 chunk 14 optimal weight: 4.9990 chunk 41 optimal weight: 0.9990 chunk 17 optimal weight: 4.9990 chunk 71 optimal weight: 6.9990 chunk 59 optimal weight: 5.9990 chunk 33 optimal weight: 0.8980 chunk 5 optimal weight: 0.9990 chunk 23 optimal weight: 5.9990 chunk 37 optimal weight: 5.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN E 68 GLN E 125 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.3383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 9605 Z= 0.287 Angle : 0.600 7.284 13907 Z= 0.359 Chirality : 0.035 0.130 1579 Planarity : 0.004 0.045 999 Dihedral : 31.442 175.096 3019 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 5.12 % Allowed : 21.32 % Favored : 73.56 % 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: 3.17 (0.36), residues: 548 helix: 2.82 (0.26), residues: 405 sheet: None (None), residues: 0 loop : -0.08 (0.50), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 75 PHE 0.008 0.001 PHE E 67 TYR 0.010 0.001 TYR D 80 ARG 0.009 0.000 ARG B 35 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 469 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 127 time to evaluate : 0.689 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 53 GLU cc_start: 0.8372 (tp30) cc_final: 0.8090 (tp30) REVERT: B 74 GLU cc_start: 0.8012 (mt-10) cc_final: 0.7776 (mt-10) REVERT: C 56 GLU cc_start: 0.8315 (OUTLIER) cc_final: 0.8012 (tt0) REVERT: C 64 GLU cc_start: 0.8851 (OUTLIER) cc_final: 0.8138 (tp30) REVERT: E 118 THR cc_start: 0.9391 (m) cc_final: 0.9168 (p) REVERT: E 129 ARG cc_start: 0.8609 (OUTLIER) cc_final: 0.8297 (tpt-90) outliers start: 24 outliers final: 16 residues processed: 137 average time/residue: 1.5699 time to fit residues: 225.8663 Evaluate side-chains 143 residues out of total 469 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 124 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain B residue 31 LYS Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 129 ARG Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 73 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 69 optimal weight: 6.9990 chunk 8 optimal weight: 2.9990 chunk 40 optimal weight: 4.9990 chunk 52 optimal weight: 10.0000 chunk 60 optimal weight: 6.9990 chunk 39 optimal weight: 0.9980 chunk 71 optimal weight: 6.9990 chunk 44 optimal weight: 4.9990 chunk 43 optimal weight: 0.3980 chunk 32 optimal weight: 8.9990 chunk 28 optimal weight: 0.8980 overall best weight: 2.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN E 68 GLN E 125 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.3415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 9605 Z= 0.250 Angle : 0.598 7.944 13907 Z= 0.357 Chirality : 0.034 0.127 1579 Planarity : 0.005 0.069 999 Dihedral : 31.403 174.483 3019 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 5.12 % Allowed : 21.75 % Favored : 73.13 % 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: 3.22 (0.36), residues: 548 helix: 2.84 (0.26), residues: 405 sheet: None (None), residues: 0 loop : -0.02 (0.50), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 75 PHE 0.008 0.001 PHE E 67 TYR 0.012 0.001 TYR D 80 ARG 0.011 0.000 ARG B 92 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 469 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 124 time to evaluate : 0.686 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 53 GLU cc_start: 0.8352 (tp30) cc_final: 0.8087 (tp30) REVERT: B 74 GLU cc_start: 0.8008 (mt-10) cc_final: 0.7696 (mt-10) REVERT: C 56 GLU cc_start: 0.8309 (OUTLIER) cc_final: 0.8005 (tt0) REVERT: E 118 THR cc_start: 0.9387 (m) cc_final: 0.9184 (p) REVERT: E 129 ARG cc_start: 0.8601 (OUTLIER) cc_final: 0.8149 (tpt-90) outliers start: 24 outliers final: 17 residues processed: 134 average time/residue: 1.5259 time to fit residues: 214.8199 Evaluate side-chains 141 residues out of total 469 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 122 time to evaluate : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain B residue 31 LYS Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 44 GLN Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 129 ARG Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 73 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 42 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 chunk 13 optimal weight: 2.9990 chunk 45 optimal weight: 0.5980 chunk 48 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 56 optimal weight: 6.9990 chunk 64 optimal weight: 8.9990 chunk 68 optimal weight: 6.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN E 68 GLN E 125 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.3456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 9605 Z= 0.194 Angle : 0.593 8.584 13907 Z= 0.353 Chirality : 0.034 0.125 1579 Planarity : 0.005 0.063 999 Dihedral : 31.385 174.202 3019 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 4.90 % Allowed : 22.39 % Favored : 72.71 % 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: 3.29 (0.36), residues: 548 helix: 2.91 (0.25), residues: 404 sheet: None (None), residues: 0 loop : 0.00 (0.50), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 75 PHE 0.008 0.001 PHE E 67 TYR 0.013 0.002 TYR D 80 ARG 0.009 0.000 ARG D 83 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 469 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 128 time to evaluate : 0.620 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 53 GLU cc_start: 0.8326 (tp30) cc_final: 0.8108 (tp30) REVERT: B 74 GLU cc_start: 0.8012 (mt-10) cc_final: 0.7719 (mt-10) REVERT: C 56 GLU cc_start: 0.8297 (OUTLIER) cc_final: 0.7991 (tt0) outliers start: 23 outliers final: 20 residues processed: 137 average time/residue: 1.5278 time to fit residues: 220.2272 Evaluate side-chains 146 residues out of total 469 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 125 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain B residue 31 LYS Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 44 GLN Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 92 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 62 optimal weight: 10.0000 chunk 66 optimal weight: 6.9990 chunk 68 optimal weight: 6.9990 chunk 40 optimal weight: 5.9990 chunk 28 optimal weight: 3.9990 chunk 52 optimal weight: 10.0000 chunk 20 optimal weight: 5.9990 chunk 60 optimal weight: 6.9990 chunk 43 optimal weight: 4.9990 chunk 70 optimal weight: 6.9990 chunk 42 optimal weight: 0.9980 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN E 68 GLN E 125 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 moved from start: 0.3546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.041 9605 Z= 0.426 Angle : 0.653 8.457 13907 Z= 0.383 Chirality : 0.038 0.134 1579 Planarity : 0.005 0.049 999 Dihedral : 31.506 170.409 3019 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 5.12 % Allowed : 22.17 % Favored : 72.71 % 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: 3.09 (0.36), residues: 548 helix: 2.76 (0.26), residues: 404 sheet: None (None), residues: 0 loop : -0.08 (0.51), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 75 PHE 0.008 0.002 PHE E 67 TYR 0.009 0.002 TYR E 54 ARG 0.010 0.001 ARG D 83 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 469 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 121 time to evaluate : 0.696 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 64 LYS cc_start: 0.9032 (OUTLIER) cc_final: 0.8711 (mttm) REVERT: B 53 GLU cc_start: 0.8398 (tp30) cc_final: 0.8165 (tp30) REVERT: B 74 GLU cc_start: 0.8010 (mt-10) cc_final: 0.7765 (mt-10) REVERT: C 56 GLU cc_start: 0.8367 (OUTLIER) cc_final: 0.8063 (tt0) REVERT: E 129 ARG cc_start: 0.8622 (OUTLIER) cc_final: 0.8308 (tpt-90) outliers start: 24 outliers final: 17 residues processed: 131 average time/residue: 1.4738 time to fit residues: 203.1316 Evaluate side-chains 138 residues out of total 469 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 118 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain B residue 31 LYS Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 44 GLN Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 129 ARG Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 73 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 33 optimal weight: 0.7980 chunk 48 optimal weight: 0.9990 chunk 73 optimal weight: 10.0000 chunk 67 optimal weight: 5.9990 chunk 58 optimal weight: 5.9990 chunk 6 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 35 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 62 optimal weight: 10.0000 chunk 17 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN E 68 GLN E 125 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.3597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 9605 Z= 0.192 Angle : 0.609 8.319 13907 Z= 0.362 Chirality : 0.035 0.128 1579 Planarity : 0.004 0.046 999 Dihedral : 31.528 170.333 3019 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 4.05 % Allowed : 23.24 % Favored : 72.71 % 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: 3.09 (0.36), residues: 548 helix: 2.74 (0.25), residues: 403 sheet: None (None), residues: 0 loop : -0.01 (0.50), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 31 PHE 0.009 0.001 PHE E 67 TYR 0.013 0.002 TYR F 88 ARG 0.011 0.001 ARG B 35 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 469 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 127 time to evaluate : 0.744 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 53 GLU cc_start: 0.8321 (tp30) cc_final: 0.8071 (tp30) REVERT: B 74 GLU cc_start: 0.7990 (mt-10) cc_final: 0.7753 (mt-10) REVERT: C 56 GLU cc_start: 0.8305 (OUTLIER) cc_final: 0.8001 (tt0) REVERT: D 90 GLU cc_start: 0.7758 (mp0) cc_final: 0.7363 (mp0) REVERT: E 129 ARG cc_start: 0.8589 (OUTLIER) cc_final: 0.8122 (tpt-90) outliers start: 19 outliers final: 16 residues processed: 135 average time/residue: 1.5254 time to fit residues: 216.6795 Evaluate side-chains 144 residues out of total 469 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 126 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain B residue 31 LYS Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain D residue 44 GLN Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 129 ARG Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 73 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 54 optimal weight: 7.9990 chunk 8 optimal weight: 0.7980 chunk 16 optimal weight: 9.9990 chunk 58 optimal weight: 6.9990 chunk 24 optimal weight: 2.9990 chunk 60 optimal weight: 6.9990 chunk 7 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 51 optimal weight: 0.9980 chunk 3 optimal weight: 0.9980 chunk 42 optimal weight: 2.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN A 125 GLN E 108 ASN E 125 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.079665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.054509 restraints weight = 23811.136| |-----------------------------------------------------------------------------| r_work (start): 0.2914 rms_B_bonded: 2.07 r_work: 0.2714 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8878 moved from start: 0.3652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9605 Z= 0.201 Angle : 0.597 8.420 13907 Z= 0.356 Chirality : 0.033 0.124 1579 Planarity : 0.004 0.043 999 Dihedral : 31.191 167.619 3019 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 3.62 % Allowed : 24.31 % Favored : 72.07 % 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: 3.30 (0.36), residues: 548 helix: 2.91 (0.25), residues: 404 sheet: None (None), residues: 0 loop : 0.01 (0.50), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 75 PHE 0.009 0.001 PHE E 67 TYR 0.009 0.001 TYR D 80 ARG 0.012 0.000 ARG B 35 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3628.78 seconds wall clock time: 370 minutes 58.05 seconds (22258.05 seconds total)