Starting phenix.real_space_refine on Wed Sep 25 19:23:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nl0_12453/09_2024/7nl0_12453.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nl0_12453/09_2024/7nl0_12453.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nl0_12453/09_2024/7nl0_12453.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nl0_12453/09_2024/7nl0_12453.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nl0_12453/09_2024/7nl0_12453.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nl0_12453/09_2024/7nl0_12453.cif" } resolution = 3.5 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= 0.001 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 262 5.49 5 S 14 5.16 5 C 6334 2.51 5 N 2121 2.21 5 O 2632 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 11363 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" 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: "B" 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: "C" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 810 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "D" Number of atoms: 746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 746 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "E" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 799 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "F" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 638 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "G" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 819 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "H" Number of atoms: 746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 746 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "I" Number of atoms: 2715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 2715 Classifications: {'DNA': 131} Link IDs: {'rna3p': 130} Chain: "J" Number of atoms: 2656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 2656 Classifications: {'DNA': 131} Link IDs: {'rna3p': 130} Time building chain proxies: 6.74, per 1000 atoms: 0.59 Number of scatterers: 11363 At special positions: 0 Unit cell: (75.9676, 120.12, 116.873, 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 14 16.00 P 262 15.00 O 2632 8.00 N 2121 7.00 C 6334 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.53 Conformation dependent library (CDL) restraints added in 825.4 milliseconds 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1406 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 9 sheets defined 73.0% alpha, 2.4% beta 127 base pairs and 223 stacking pairs defined. Time for finding SS restraints: 4.90 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 77 removed outlier: 3.820A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (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 removed outlier: 3.671A pdb=" N GLN B 27 " --> pdb=" O ASP B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.802A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 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: 4.505A 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 92 through 97 Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 53 through 81 Processing helix chain 'D' and resid 87 through 99 removed outlier: 3.591A pdb=" N ILE D 91 " --> pdb=" O THR D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 121 Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 79 removed outlier: 3.500A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (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 removed outlier: 3.787A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.638A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 46 through 73 removed outlier: 3.727A pdb=" N ASN G 73 " --> pdb=" O ALA G 69 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'G' and resid 112 through 116 removed outlier: 3.513A pdb=" N LEU G 116 " --> pdb=" O ALA G 113 " (cutoff:3.500A) Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 100 through 120 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.350A 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 'B' and resid 97 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.413A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 101 through 102 removed outlier: 6.676A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.283A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 77 through 78 409 hydrogen bonds defined for protein. 1212 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 307 hydrogen bonds 614 hydrogen bond angles 0 basepair planarities 127 basepair parallelities 223 stacking parallelities Total time for adding SS restraints: 3.82 Time building geometry restraints manager: 3.01 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: 2176 1.33 - 1.45: 3809 1.45 - 1.57: 5564 1.57 - 1.69: 522 1.69 - 1.81: 24 Bond restraints: 12095 Sorted by residual: bond pdb=" C3' DA I 58 " pdb=" O3' DA I 58 " ideal model delta sigma weight residual 1.422 1.481 -0.059 3.00e-02 1.11e+03 3.88e+00 bond pdb=" CG1 ILE H 86 " pdb=" CD1 ILE H 86 " ideal model delta sigma weight residual 1.513 1.446 0.067 3.90e-02 6.57e+02 2.94e+00 bond pdb=" C3' DA I 14 " pdb=" O3' DA I 14 " ideal model delta sigma weight residual 1.422 1.472 -0.050 3.00e-02 1.11e+03 2.81e+00 bond pdb=" CG1 ILE D 86 " pdb=" CD1 ILE D 86 " ideal model delta sigma weight residual 1.513 1.452 0.061 3.90e-02 6.57e+02 2.49e+00 bond pdb=" C3' DC J -52 " pdb=" O3' DC J -52 " ideal model delta sigma weight residual 1.422 1.462 -0.040 3.00e-02 1.11e+03 1.78e+00 ... (remaining 12090 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.61: 16646 1.61 - 3.21: 753 3.21 - 4.82: 36 4.82 - 6.43: 15 6.43 - 8.04: 1 Bond angle restraints: 17451 Sorted by residual: angle pdb=" N VAL A 117 " pdb=" CA VAL A 117 " pdb=" C VAL A 117 " ideal model delta sigma weight residual 113.71 107.75 5.96 9.50e-01 1.11e+00 3.94e+01 angle pdb=" C GLY G 37 " pdb=" N ASN G 38 " pdb=" CA ASN G 38 " ideal model delta sigma weight residual 121.54 127.28 -5.74 1.91e+00 2.74e-01 9.04e+00 angle pdb=" CA VAL A 117 " pdb=" C VAL A 117 " pdb=" N THR A 118 " ideal model delta sigma weight residual 119.87 116.36 3.51 1.34e+00 5.57e-01 6.87e+00 angle pdb=" C3' DA I 58 " pdb=" O3' DA I 58 " pdb=" P DT I 59 " ideal model delta sigma weight residual 120.20 124.04 -3.84 1.50e+00 4.44e-01 6.54e+00 angle pdb=" C3' DA I 14 " pdb=" O3' DA I 14 " pdb=" P DA I 15 " ideal model delta sigma weight residual 120.20 123.98 -3.78 1.50e+00 4.44e-01 6.34e+00 ... (remaining 17446 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.14: 5243 35.14 - 70.28: 1400 70.28 - 105.43: 23 105.43 - 140.57: 3 140.57 - 175.71: 9 Dihedral angle restraints: 6678 sinusoidal: 4495 harmonic: 2183 Sorted by residual: dihedral pdb=" CA TYR G 39 " pdb=" C TYR G 39 " pdb=" N SER G 40 " pdb=" CA SER G 40 " ideal model delta harmonic sigma weight residual 180.00 159.30 20.70 0 5.00e+00 4.00e-02 1.71e+01 dihedral pdb=" C4' DG J 30 " pdb=" C3' DG J 30 " pdb=" O3' DG J 30 " pdb=" P DA J 31 " ideal model delta sinusoidal sigma weight residual -140.00 35.71 -175.71 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DT I -17 " pdb=" C3' DT I -17 " pdb=" O3' DT I -17 " pdb=" P DG I -16 " ideal model delta sinusoidal sigma weight residual -140.00 33.83 -173.83 1 3.50e+01 8.16e-04 1.56e+01 ... (remaining 6675 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1249 0.032 - 0.065: 536 0.065 - 0.097: 147 0.097 - 0.129: 47 0.129 - 0.161: 4 Chirality restraints: 1983 Sorted by residual: chirality pdb=" CA ASN G 38 " pdb=" N ASN G 38 " pdb=" C ASN G 38 " pdb=" CB ASN G 38 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.50e-01 chirality pdb=" P DT I 59 " pdb=" OP1 DT I 59 " pdb=" OP2 DT I 59 " pdb=" O5' DT I 59 " both_signs ideal model delta sigma weight residual True 2.35 -2.48 -0.13 2.00e-01 2.50e+01 4.41e-01 chirality pdb=" CA VAL C 107 " pdb=" N VAL C 107 " pdb=" C VAL C 107 " pdb=" CB VAL C 107 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.40e-01 ... (remaining 1980 not shown) Planarity restraints: 1305 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DA I -24 " -0.027 2.00e-02 2.50e+03 1.18e-02 3.80e+00 pdb=" N9 DA I -24 " 0.025 2.00e-02 2.50e+03 pdb=" C8 DA I -24 " 0.002 2.00e-02 2.50e+03 pdb=" N7 DA I -24 " 0.005 2.00e-02 2.50e+03 pdb=" C5 DA I -24 " -0.002 2.00e-02 2.50e+03 pdb=" C6 DA I -24 " -0.004 2.00e-02 2.50e+03 pdb=" N6 DA I -24 " -0.010 2.00e-02 2.50e+03 pdb=" N1 DA I -24 " -0.001 2.00e-02 2.50e+03 pdb=" C2 DA I -24 " 0.004 2.00e-02 2.50e+03 pdb=" N3 DA I -24 " 0.005 2.00e-02 2.50e+03 pdb=" C4 DA I -24 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG I 16 " 0.027 2.00e-02 2.50e+03 1.10e-02 3.66e+00 pdb=" N9 DG I 16 " -0.018 2.00e-02 2.50e+03 pdb=" C8 DG I 16 " -0.003 2.00e-02 2.50e+03 pdb=" N7 DG I 16 " -0.008 2.00e-02 2.50e+03 pdb=" C5 DG I 16 " -0.006 2.00e-02 2.50e+03 pdb=" C6 DG I 16 " 0.006 2.00e-02 2.50e+03 pdb=" O6 DG I 16 " 0.013 2.00e-02 2.50e+03 pdb=" N1 DG I 16 " 0.004 2.00e-02 2.50e+03 pdb=" C2 DG I 16 " -0.004 2.00e-02 2.50e+03 pdb=" N2 DG I 16 " -0.004 2.00e-02 2.50e+03 pdb=" N3 DG I 16 " -0.003 2.00e-02 2.50e+03 pdb=" C4 DG I 16 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG I 28 " 0.025 2.00e-02 2.50e+03 1.08e-02 3.50e+00 pdb=" N9 DG I 28 " -0.026 2.00e-02 2.50e+03 pdb=" C8 DG I 28 " -0.003 2.00e-02 2.50e+03 pdb=" N7 DG I 28 " -0.001 2.00e-02 2.50e+03 pdb=" C5 DG I 28 " 0.000 2.00e-02 2.50e+03 pdb=" C6 DG I 28 " 0.004 2.00e-02 2.50e+03 pdb=" O6 DG I 28 " 0.008 2.00e-02 2.50e+03 pdb=" N1 DG I 28 " 0.001 2.00e-02 2.50e+03 pdb=" C2 DG I 28 " -0.002 2.00e-02 2.50e+03 pdb=" N2 DG I 28 " -0.002 2.00e-02 2.50e+03 pdb=" N3 DG I 28 " -0.002 2.00e-02 2.50e+03 pdb=" C4 DG I 28 " -0.002 2.00e-02 2.50e+03 ... (remaining 1302 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 559 2.70 - 3.25: 9965 3.25 - 3.80: 22342 3.80 - 4.35: 27582 4.35 - 4.90: 39438 Nonbonded interactions: 99886 Sorted by model distance: nonbonded pdb=" OD2 ASP D 65 " pdb=" OH TYR F 98 " model vdw 2.147 3.040 nonbonded pdb=" OD1 ASP C 90 " pdb=" N GLU C 91 " model vdw 2.185 3.120 nonbonded pdb=" NE ARG A 131 " pdb=" OE2 GLU A 133 " model vdw 2.233 3.120 nonbonded pdb=" OH TYR A 99 " pdb=" OE1 GLU A 133 " model vdw 2.237 3.040 nonbonded pdb=" OD2 ASP E 106 " pdb=" NH1 ARG E 131 " model vdw 2.251 3.120 ... (remaining 99881 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 39 through 134 or (resid 135 and (name N or name CA or nam \ e C or name O or name CB )))) selection = chain 'E' } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 24 through 102) } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 13 through 117) } ncs_group { reference = chain 'D' selection = chain 'H' } 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: 2.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.430 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 29.060 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.040 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:2.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 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 : 0.006 0.067 12095 Z= 0.368 Angle : 0.709 8.036 17451 Z= 0.428 Chirality : 0.039 0.161 1983 Planarity : 0.004 0.040 1305 Dihedral : 29.742 175.712 5272 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % 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: 0.67 (0.30), residues: 739 helix: 1.29 (0.22), residues: 537 sheet: None (None), residues: 0 loop : -1.90 (0.39), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS H 79 PHE 0.024 0.003 PHE C 25 TYR 0.012 0.002 TYR F 51 ARG 0.005 0.000 ARG G 32 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 132 time to evaluate : 0.935 Fit side-chains REVERT: E 59 GLU cc_start: 0.7178 (pp20) cc_final: 0.6897 (pm20) outliers start: 0 outliers final: 0 residues processed: 132 average time/residue: 0.3418 time to fit residues: 58.0472 Evaluate side-chains 121 residues out of total 627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 121 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 81 optimal weight: 4.9990 chunk 73 optimal weight: 6.9990 chunk 40 optimal weight: 0.7980 chunk 25 optimal weight: 0.6980 chunk 49 optimal weight: 0.6980 chunk 39 optimal weight: 1.9990 chunk 76 optimal weight: 4.9990 chunk 29 optimal weight: 0.4980 chunk 46 optimal weight: 0.9990 chunk 56 optimal weight: 0.9990 chunk 88 optimal weight: 5.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 92 GLN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.0668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 12095 Z= 0.215 Angle : 0.646 8.570 17451 Z= 0.379 Chirality : 0.037 0.153 1983 Planarity : 0.004 0.037 1305 Dihedral : 32.882 175.280 3777 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.28 % Allowed : 7.66 % Favored : 91.07 % 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: 1.27 (0.31), residues: 739 helix: 1.70 (0.22), residues: 548 sheet: None (None), residues: 0 loop : -1.75 (0.40), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS F 75 PHE 0.013 0.002 PHE C 25 TYR 0.016 0.002 TYR C 57 ARG 0.005 0.000 ARG A 128 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 132 time to evaluate : 0.951 Fit side-chains REVERT: E 59 GLU cc_start: 0.7207 (pp20) cc_final: 0.6974 (pm20) outliers start: 8 outliers final: 7 residues processed: 134 average time/residue: 0.3422 time to fit residues: 59.0724 Evaluate side-chains 130 residues out of total 627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 123 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 36 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 48 optimal weight: 0.7980 chunk 27 optimal weight: 3.9990 chunk 73 optimal weight: 7.9990 chunk 59 optimal weight: 0.8980 chunk 24 optimal weight: 5.9990 chunk 88 optimal weight: 6.9990 chunk 95 optimal weight: 6.9990 chunk 78 optimal weight: 7.9990 chunk 87 optimal weight: 5.9990 chunk 30 optimal weight: 0.9980 chunk 70 optimal weight: 2.9990 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 38 ASN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.0758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 12095 Z= 0.320 Angle : 0.659 6.887 17451 Z= 0.383 Chirality : 0.037 0.153 1983 Planarity : 0.004 0.036 1305 Dihedral : 32.842 177.331 3777 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.07 % Allowed : 10.69 % Favored : 87.24 % 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: 1.42 (0.31), residues: 739 helix: 1.88 (0.22), residues: 544 sheet: None (None), residues: 0 loop : -1.85 (0.39), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS G 31 PHE 0.014 0.003 PHE A 67 TYR 0.011 0.002 TYR F 51 ARG 0.004 0.000 ARG F 35 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 123 time to evaluate : 0.802 Fit side-chains REVERT: E 59 GLU cc_start: 0.7231 (pp20) cc_final: 0.7029 (pm20) outliers start: 13 outliers final: 11 residues processed: 126 average time/residue: 0.3134 time to fit residues: 51.5304 Evaluate side-chains 131 residues out of total 627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 120 time to evaluate : 0.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain C residue 38 ASN Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 115 LYS Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain H residue 87 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 87 optimal weight: 5.9990 chunk 66 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 9 optimal weight: 0.9980 chunk 42 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 chunk 88 optimal weight: 6.9990 chunk 93 optimal weight: 5.9990 chunk 46 optimal weight: 0.9990 chunk 83 optimal weight: 9.9990 chunk 25 optimal weight: 0.8980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.1023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 12095 Z= 0.209 Angle : 0.605 6.361 17451 Z= 0.359 Chirality : 0.036 0.147 1983 Planarity : 0.004 0.039 1305 Dihedral : 32.782 178.531 3777 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.39 % Allowed : 11.64 % Favored : 85.96 % 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: 1.83 (0.31), residues: 739 helix: 2.15 (0.22), residues: 548 sheet: None (None), residues: 0 loop : -1.69 (0.40), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS G 31 PHE 0.013 0.002 PHE A 67 TYR 0.023 0.002 TYR C 39 ARG 0.003 0.000 ARG G 71 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 135 time to evaluate : 0.862 Fit side-chains outliers start: 15 outliers final: 13 residues processed: 140 average time/residue: 0.3041 time to fit residues: 55.7723 Evaluate side-chains 140 residues out of total 627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 127 time to evaluate : 1.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain D residue 82 LYS Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 115 LYS Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 87 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 78 optimal weight: 7.9990 chunk 53 optimal weight: 4.9990 chunk 1 optimal weight: 0.7980 chunk 69 optimal weight: 0.3980 chunk 38 optimal weight: 0.7980 chunk 80 optimal weight: 6.9990 chunk 64 optimal weight: 4.9990 chunk 0 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 chunk 84 optimal weight: 10.0000 chunk 23 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.1279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 12095 Z= 0.192 Angle : 0.595 5.670 17451 Z= 0.354 Chirality : 0.035 0.134 1983 Planarity : 0.004 0.042 1305 Dihedral : 32.694 179.492 3777 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.75 % Allowed : 12.60 % Favored : 85.65 % 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: 2.09 (0.31), residues: 739 helix: 2.34 (0.21), residues: 548 sheet: None (None), residues: 0 loop : -1.60 (0.41), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS G 31 PHE 0.014 0.002 PHE A 67 TYR 0.012 0.001 TYR C 57 ARG 0.003 0.000 ARG H 83 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 134 time to evaluate : 0.813 Fit side-chains REVERT: D 32 GLU cc_start: 0.8402 (mm-30) cc_final: 0.8181 (mm-30) REVERT: H 69 ARG cc_start: 0.8471 (mtm-85) cc_final: 0.8210 (mtm180) outliers start: 11 outliers final: 9 residues processed: 136 average time/residue: 0.3122 time to fit residues: 55.7204 Evaluate side-chains 134 residues out of total 627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 125 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain E residue 115 LYS Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 72 ASP Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 87 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 31 optimal weight: 0.0970 chunk 84 optimal weight: 10.0000 chunk 18 optimal weight: 0.8980 chunk 55 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 93 optimal weight: 5.9990 chunk 77 optimal weight: 6.9990 chunk 43 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 49 optimal weight: 0.7980 chunk 90 optimal weight: 4.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.1433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 12095 Z= 0.187 Angle : 0.590 7.904 17451 Z= 0.350 Chirality : 0.035 0.136 1983 Planarity : 0.004 0.040 1305 Dihedral : 32.643 179.909 3777 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.07 % Allowed : 12.92 % Favored : 85.01 % 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: 2.24 (0.31), residues: 739 helix: 2.42 (0.21), residues: 548 sheet: None (None), residues: 0 loop : -1.47 (0.41), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS G 31 PHE 0.014 0.002 PHE A 67 TYR 0.013 0.001 TYR C 57 ARG 0.004 0.000 ARG H 83 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 126 time to evaluate : 0.856 Fit side-chains REVERT: H 69 ARG cc_start: 0.8470 (mtm-85) cc_final: 0.8248 (mtm180) REVERT: H 90 GLU cc_start: 0.8033 (OUTLIER) cc_final: 0.7351 (mt-10) outliers start: 13 outliers final: 11 residues processed: 130 average time/residue: 0.3335 time to fit residues: 57.2258 Evaluate side-chains 137 residues out of total 627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 125 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain D residue 82 LYS Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain E residue 115 LYS Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 72 ASP Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 90 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 10 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 79 optimal weight: 8.9990 chunk 52 optimal weight: 0.9990 chunk 93 optimal weight: 5.9990 chunk 58 optimal weight: 0.9980 chunk 56 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.1431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 12095 Z= 0.242 Angle : 0.604 6.575 17451 Z= 0.357 Chirality : 0.036 0.151 1983 Planarity : 0.004 0.040 1305 Dihedral : 32.629 179.999 3777 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.23 % Allowed : 14.35 % Favored : 83.41 % 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: 2.13 (0.30), residues: 739 helix: 2.38 (0.21), residues: 546 sheet: None (None), residues: 0 loop : -1.59 (0.40), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS G 31 PHE 0.013 0.002 PHE A 67 TYR 0.012 0.001 TYR C 57 ARG 0.003 0.000 ARG H 83 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 127 time to evaluate : 0.903 Fit side-chains REVERT: B 79 LYS cc_start: 0.8166 (OUTLIER) cc_final: 0.7677 (mtmm) REVERT: H 69 ARG cc_start: 0.8485 (mtm-85) cc_final: 0.8235 (mtm180) REVERT: H 90 GLU cc_start: 0.8063 (OUTLIER) cc_final: 0.7410 (mt-10) outliers start: 14 outliers final: 10 residues processed: 133 average time/residue: 0.3139 time to fit residues: 54.9687 Evaluate side-chains 136 residues out of total 627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 124 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain E residue 115 LYS Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 90 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 55 optimal weight: 0.5980 chunk 28 optimal weight: 0.8980 chunk 18 optimal weight: 0.0670 chunk 59 optimal weight: 0.9980 chunk 63 optimal weight: 0.8980 chunk 46 optimal weight: 0.6980 chunk 8 optimal weight: 0.9990 chunk 73 optimal weight: 6.9990 chunk 85 optimal weight: 7.9990 chunk 89 optimal weight: 6.9990 chunk 81 optimal weight: 5.9990 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.1563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 12095 Z= 0.179 Angle : 0.588 8.454 17451 Z= 0.349 Chirality : 0.035 0.135 1983 Planarity : 0.004 0.041 1305 Dihedral : 32.578 179.557 3777 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.23 % Allowed : 14.67 % Favored : 83.09 % 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: 2.31 (0.31), residues: 739 helix: 2.47 (0.21), residues: 548 sheet: None (None), residues: 0 loop : -1.41 (0.41), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS G 31 PHE 0.012 0.002 PHE A 67 TYR 0.010 0.001 TYR C 57 ARG 0.003 0.000 ARG H 83 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 126 time to evaluate : 0.822 Fit side-chains REVERT: B 79 LYS cc_start: 0.8142 (OUTLIER) cc_final: 0.7661 (mtmm) REVERT: E 56 LYS cc_start: 0.7812 (mtmt) cc_final: 0.7547 (mtmt) REVERT: H 69 ARG cc_start: 0.8472 (mtm-85) cc_final: 0.8251 (mtm180) REVERT: H 90 GLU cc_start: 0.8014 (OUTLIER) cc_final: 0.7330 (mt-10) outliers start: 14 outliers final: 11 residues processed: 132 average time/residue: 0.3153 time to fit residues: 54.6987 Evaluate side-chains 138 residues out of total 627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 125 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain E residue 115 LYS Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 72 ASP Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 90 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 87 optimal weight: 5.9990 chunk 89 optimal weight: 6.9990 chunk 52 optimal weight: 9.9990 chunk 37 optimal weight: 0.0030 chunk 68 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 78 optimal weight: 4.9990 chunk 82 optimal weight: 7.9990 chunk 86 optimal weight: 4.9990 chunk 57 optimal weight: 1.9990 chunk 92 optimal weight: 4.9990 overall best weight: 2.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.1373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.071 12095 Z= 0.397 Angle : 0.680 7.925 17451 Z= 0.391 Chirality : 0.039 0.162 1983 Planarity : 0.005 0.037 1305 Dihedral : 32.770 177.919 3777 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 2.55 % Allowed : 14.51 % Favored : 82.93 % 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: 1.70 (0.30), residues: 739 helix: 2.01 (0.21), residues: 548 sheet: None (None), residues: 0 loop : -1.58 (0.39), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.002 HIS G 31 PHE 0.018 0.003 PHE G 25 TYR 0.013 0.002 TYR D 118 ARG 0.003 0.000 ARG D 89 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 125 time to evaluate : 0.944 Fit side-chains REVERT: B 79 LYS cc_start: 0.8252 (OUTLIER) cc_final: 0.7824 (mtmm) REVERT: H 90 GLU cc_start: 0.8089 (OUTLIER) cc_final: 0.7340 (mp0) outliers start: 16 outliers final: 12 residues processed: 134 average time/residue: 0.3154 time to fit residues: 55.3468 Evaluate side-chains 137 residues out of total 627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 123 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain E residue 115 LYS Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 90 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 56 optimal weight: 0.8980 chunk 43 optimal weight: 1.9990 chunk 64 optimal weight: 0.7980 chunk 96 optimal weight: 8.9990 chunk 88 optimal weight: 6.9990 chunk 76 optimal weight: 4.9990 chunk 7 optimal weight: 0.8980 chunk 59 optimal weight: 0.7980 chunk 47 optimal weight: 0.7980 chunk 61 optimal weight: 0.5980 chunk 81 optimal weight: 5.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.1790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 12095 Z= 0.192 Angle : 0.590 6.470 17451 Z= 0.349 Chirality : 0.035 0.139 1983 Planarity : 0.004 0.041 1305 Dihedral : 32.440 178.225 3777 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.75 % Allowed : 15.79 % Favored : 82.46 % 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: 2.33 (0.31), residues: 739 helix: 2.43 (0.21), residues: 547 sheet: None (None), residues: 0 loop : -1.19 (0.43), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS F 75 PHE 0.015 0.002 PHE A 67 TYR 0.018 0.001 TYR C 57 ARG 0.003 0.000 ARG H 83 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 132 time to evaluate : 0.889 Fit side-chains REVERT: B 79 LYS cc_start: 0.8167 (OUTLIER) cc_final: 0.7701 (mtmm) REVERT: H 69 ARG cc_start: 0.8484 (mtm-85) cc_final: 0.8262 (mtm180) REVERT: H 90 GLU cc_start: 0.8012 (OUTLIER) cc_final: 0.7374 (mp0) outliers start: 11 outliers final: 8 residues processed: 138 average time/residue: 0.3040 time to fit residues: 55.3511 Evaluate side-chains 135 residues out of total 627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 125 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 90 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 23 optimal weight: 0.0870 chunk 70 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 77 optimal weight: 6.9990 chunk 32 optimal weight: 1.9990 chunk 79 optimal weight: 8.9990 chunk 9 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 chunk 67 optimal weight: 3.9990 chunk 4 optimal weight: 0.0870 overall best weight: 0.7938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.143679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.104948 restraints weight = 18519.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.107632 restraints weight = 11325.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.109243 restraints weight = 8674.236| |-----------------------------------------------------------------------------| r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.1931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 12095 Z= 0.190 Angle : 0.586 7.147 17451 Z= 0.347 Chirality : 0.034 0.140 1983 Planarity : 0.004 0.041 1305 Dihedral : 32.406 178.038 3777 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.07 % Allowed : 14.83 % Favored : 83.09 % 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: 2.56 (0.31), residues: 739 helix: 2.59 (0.21), residues: 548 sheet: None (None), residues: 0 loop : -1.08 (0.44), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS F 75 PHE 0.014 0.002 PHE A 67 TYR 0.017 0.001 TYR C 57 ARG 0.003 0.000 ARG H 83 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1964.72 seconds wall clock time: 36 minutes 20.89 seconds (2180.89 seconds total)