Starting phenix.real_space_refine on Fri Mar 15 21:14:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8peo_17633/03_2024/8peo_17633_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8peo_17633/03_2024/8peo_17633.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.69 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8peo_17633/03_2024/8peo_17633.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8peo_17633/03_2024/8peo_17633.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8peo_17633/03_2024/8peo_17633_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8peo_17633/03_2024/8peo_17633_updated.pdb" } resolution = 2.69 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.013 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 294 5.49 5 S 13 5.16 5 C 7171 2.51 5 N 2399 2.21 5 O 2958 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 50": "OE1" <-> "OE2" Residue "A GLU 97": "OE1" <-> "OE2" Residue "B GLU 63": "OE1" <-> "OE2" Residue "C GLU 41": "OE1" <-> "OE2" Residue "C GLU 91": "OE1" <-> "OE2" Residue "D GLU 32": "OE1" <-> "OE2" Residue "D GLU 68": "OE1" <-> "OE2" Residue "D GLU 73": "OE1" <-> "OE2" Residue "D GLU 110": "OE1" <-> "OE2" Residue "E GLU 50": "OE1" <-> "OE2" Residue "F GLU 63": "OE1" <-> "OE2" Residue "F GLU 74": "OE1" <-> "OE2" Residue "G GLU 41": "OE1" <-> "OE2" Residue "G GLU 56": "OE1" <-> "OE2" Residue "G GLU 61": "OE1" <-> "OE2" Residue "G GLU 64": "OE1" <-> "OE2" Residue "H GLU 73": "OE1" <-> "OE2" Residue "H GLU 90": "OE1" <-> "OE2" Residue "H GLU 102": "OE1" <-> "OE2" Residue "H GLU 110": "OE1" <-> "OE2" Residue "K GLU 83": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 12835 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 817 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain breaks: 1 Chain: "B" Number of atoms: 657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 657 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "C" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 823 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "D" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 736 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "E" 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: "F" Number of atoms: 694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 694 Classifications: {'peptide': 86} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 84} Chain: "G" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 823 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "H" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 736 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "I" Number of atoms: 2996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 2996 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "K" Number of atoms: 710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 710 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 11, 'TRANS': 74} Chain breaks: 1 Chain: "J" Number of atoms: 3031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 3031 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "A" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Classifications: {'peptide': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'M2L:plan-1': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 6.52, per 1000 atoms: 0.51 Number of scatterers: 12835 At special positions: 0 Unit cell: (91.696, 119.205, 138.378, 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 13 16.00 P 294 15.00 O 2958 8.00 N 2399 7.00 C 7171 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 5.91 Conformation dependent library (CDL) restraints added in 1.3 seconds 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1598 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 36 helices and 1 sheets defined 57.7% alpha, 2.0% beta 146 base pairs and 270 stacking pairs defined. Time for finding SS restraints: 7.47 Creating SS restraints... Processing helix chain 'A' and resid 45 through 54 Processing helix chain 'A' and resid 64 through 76 removed outlier: 3.937A pdb=" N GLN A 76 " --> pdb=" O ARG A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 113 Processing helix chain 'A' and resid 121 through 131 Processing helix chain 'B' and resid 26 through 28 No H-bonds generated for 'chain 'B' and resid 26 through 28' Processing helix chain 'B' and resid 31 through 41 Processing helix chain 'B' and resid 50 through 75 removed outlier: 3.725A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 93 removed outlier: 3.569A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 21 Processing helix chain 'C' and resid 27 through 37 Processing helix chain 'C' and resid 47 through 72 Processing helix chain 'C' and resid 80 through 89 Processing helix chain 'C' and resid 91 through 96 Processing helix chain 'D' and resid 35 through 45 Processing helix chain 'D' and resid 53 through 81 Processing helix chain 'D' and resid 88 through 98 Processing helix chain 'D' and resid 101 through 120 removed outlier: 4.359A pdb=" N VAL D 108 " --> pdb=" O LYS D 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 54 Processing helix chain 'E' and resid 64 through 77 removed outlier: 4.436A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 113 Processing helix chain 'E' and resid 121 through 131 Processing helix chain 'F' and resid 26 through 28 No H-bonds generated for 'chain 'F' and resid 26 through 28' Processing helix chain 'F' and resid 31 through 41 Processing helix chain 'F' and resid 48 through 75 removed outlier: 4.109A pdb=" N TYR F 51 " --> pdb=" O GLY F 48 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLU F 52 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ILE F 66 " --> pdb=" O GLU F 63 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ARG F 67 " --> pdb=" O ASN F 64 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASP F 68 " --> pdb=" O VAL F 65 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 92 Processing helix chain 'G' and resid 17 through 21 Processing helix chain 'G' and resid 27 through 36 Processing helix chain 'G' and resid 45 through 72 removed outlier: 4.397A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 88 Processing helix chain 'G' and resid 93 through 96 No H-bonds generated for 'chain 'G' and resid 93 through 96' Processing helix chain 'G' and resid 113 through 115 No H-bonds generated for 'chain 'G' and resid 113 through 115' Processing helix chain 'H' and resid 35 through 45 Processing helix chain 'H' and resid 53 through 80 Processing helix chain 'H' and resid 88 through 98 Processing helix chain 'H' and resid 101 through 120 removed outlier: 4.112A pdb=" N LYS H 105 " --> pdb=" O GLY H 101 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N HIS H 106 " --> pdb=" O GLU H 102 " (cutoff:3.500A) Processing helix chain 'K' and resid 77 through 82 Processing sheet with id= A, first strand: chain 'K' and resid 58 through 60 removed outlier: 3.839A pdb=" N GLU K 49 " --> pdb=" O PHE K 44 " (cutoff:3.500A) 353 hydrogen bonds defined for protein. 945 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 374 hydrogen bonds 748 hydrogen bond angles 0 basepair planarities 146 basepair parallelities 270 stacking parallelities Total time for adding SS restraints: 4.76 Time building geometry restraints manager: 6.34 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: 2228 1.33 - 1.45: 4599 1.45 - 1.57: 6234 1.57 - 1.69: 586 1.69 - 1.82: 26 Bond restraints: 13673 Sorted by residual: bond pdb=" N ARG E 129 " pdb=" CA ARG E 129 " ideal model delta sigma weight residual 1.459 1.488 -0.028 1.20e-02 6.94e+03 5.59e+00 bond pdb=" N ASP E 123 " pdb=" CA ASP E 123 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.20e-02 6.94e+03 5.49e+00 bond pdb=" C TRP K 21 " pdb=" N PRO K 22 " ideal model delta sigma weight residual 1.332 1.358 -0.026 1.12e-02 7.97e+03 5.43e+00 bond pdb=" N ARG B 36 " pdb=" CA ARG B 36 " ideal model delta sigma weight residual 1.459 1.486 -0.027 1.20e-02 6.94e+03 5.09e+00 bond pdb=" P DG I -49 " pdb=" OP1 DG I -49 " ideal model delta sigma weight residual 1.480 1.521 -0.041 2.00e-02 2.50e+03 4.22e+00 ... (remaining 13668 not shown) Histogram of bond angle deviations from ideal: 98.08 - 105.26: 1321 105.26 - 112.43: 7523 112.43 - 119.60: 4514 119.60 - 126.77: 5533 126.77 - 133.94: 830 Bond angle restraints: 19721 Sorted by residual: angle pdb=" C ILE B 34 " pdb=" N ARG B 35 " pdb=" CA ARG B 35 " ideal model delta sigma weight residual 120.29 114.32 5.97 1.42e+00 4.96e-01 1.77e+01 angle pdb=" CA ASN G 73 " pdb=" CB ASN G 73 " pdb=" CG ASN G 73 " ideal model delta sigma weight residual 112.60 116.80 -4.20 1.00e+00 1.00e+00 1.77e+01 angle pdb=" CA ASN C 73 " pdb=" CB ASN C 73 " pdb=" CG ASN C 73 " ideal model delta sigma weight residual 112.60 116.63 -4.03 1.00e+00 1.00e+00 1.62e+01 angle pdb=" CA GLU D 68 " pdb=" CB GLU D 68 " pdb=" CG GLU D 68 " ideal model delta sigma weight residual 114.10 121.58 -7.48 2.00e+00 2.50e-01 1.40e+01 angle pdb=" C ASN G 73 " pdb=" CA ASN G 73 " pdb=" CB ASN G 73 " ideal model delta sigma weight residual 110.56 116.29 -5.73 1.69e+00 3.50e-01 1.15e+01 ... (remaining 19716 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.44: 5770 35.44 - 70.87: 1661 70.87 - 106.31: 37 106.31 - 141.74: 3 141.74 - 177.18: 4 Dihedral angle restraints: 7475 sinusoidal: 5003 harmonic: 2472 Sorted by residual: dihedral pdb=" CD M2L A 201 " pdb=" CE M2L A 201 " pdb=" NZ M2L A 201 " pdb=" CM1 M2L A 201 " ideal model delta sinusoidal sigma weight residual 66.23 -97.71 163.94 1 3.00e+01 1.11e-03 2.09e+01 dihedral pdb=" C4' DT J 69 " pdb=" C3' DT J 69 " pdb=" O3' DT J 69 " pdb=" P DC J 70 " ideal model delta sinusoidal sigma weight residual 220.00 42.82 177.18 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DC J 68 " pdb=" C3' DC J 68 " pdb=" O3' DC J 68 " pdb=" P DT J 69 " ideal model delta sinusoidal sigma weight residual -140.00 24.39 -164.39 1 3.50e+01 8.16e-04 1.54e+01 ... (remaining 7472 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.104: 2154 0.104 - 0.208: 70 0.208 - 0.313: 1 0.313 - 0.417: 0 0.417 - 0.521: 4 Chirality restraints: 2229 Sorted by residual: chirality pdb=" P DG J 50 " pdb=" OP1 DG J 50 " pdb=" OP2 DG J 50 " pdb=" O5' DG J 50 " both_signs ideal model delta sigma weight residual True 2.35 -2.87 -0.52 2.00e-01 2.50e+01 6.78e+00 chirality pdb=" P DC J 49 " pdb=" OP1 DC J 49 " pdb=" OP2 DC J 49 " pdb=" O5' DC J 49 " both_signs ideal model delta sigma weight residual True 2.35 -2.86 -0.52 2.00e-01 2.50e+01 6.67e+00 chirality pdb=" P DC I -50 " pdb=" OP1 DC I -50 " pdb=" OP2 DC I -50 " pdb=" O5' DC I -50 " both_signs ideal model delta sigma weight residual True 2.35 -2.86 -0.52 2.00e-01 2.50e+01 6.65e+00 ... (remaining 2226 not shown) Planarity restraints: 1477 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN G 73 " -0.019 2.00e-02 2.50e+03 3.88e-02 1.51e+01 pdb=" C ASN G 73 " 0.067 2.00e-02 2.50e+03 pdb=" O ASN G 73 " -0.025 2.00e-02 2.50e+03 pdb=" N LYS G 74 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC I 69 " -0.040 2.00e-02 2.50e+03 2.41e-02 1.31e+01 pdb=" N1 DC I 69 " 0.057 2.00e-02 2.50e+03 pdb=" C2 DC I 69 " -0.013 2.00e-02 2.50e+03 pdb=" O2 DC I 69 " 0.009 2.00e-02 2.50e+03 pdb=" N3 DC I 69 " -0.001 2.00e-02 2.50e+03 pdb=" C4 DC I 69 " -0.004 2.00e-02 2.50e+03 pdb=" N4 DC I 69 " -0.010 2.00e-02 2.50e+03 pdb=" C5 DC I 69 " -0.000 2.00e-02 2.50e+03 pdb=" C6 DC I 69 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC I 49 " 0.030 2.00e-02 2.50e+03 2.39e-02 1.28e+01 pdb=" N1 DC I 49 " -0.057 2.00e-02 2.50e+03 pdb=" C2 DC I 49 " 0.028 2.00e-02 2.50e+03 pdb=" O2 DC I 49 " -0.010 2.00e-02 2.50e+03 pdb=" N3 DC I 49 " -0.003 2.00e-02 2.50e+03 pdb=" C4 DC I 49 " 0.003 2.00e-02 2.50e+03 pdb=" N4 DC I 49 " 0.003 2.00e-02 2.50e+03 pdb=" C5 DC I 49 " 0.006 2.00e-02 2.50e+03 pdb=" C6 DC I 49 " -0.001 2.00e-02 2.50e+03 ... (remaining 1474 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1281 2.74 - 3.28: 10780 3.28 - 3.82: 25225 3.82 - 4.36: 30151 4.36 - 4.90: 43125 Nonbonded interactions: 110562 Sorted by model distance: nonbonded pdb=" O GLU K 66 " pdb=" NZ LYS K 70 " model vdw 2.201 2.520 nonbonded pdb=" N GLU A 59 " pdb=" OE1 GLU A 59 " model vdw 2.204 2.520 nonbonded pdb=" NZ LYS H 43 " pdb=" O THR H 49 " model vdw 2.219 2.520 nonbonded pdb=" O TRP K 82 " pdb=" ND2 ASN K 86 " model vdw 2.241 2.520 nonbonded pdb=" OG1 THR F 73 " pdb=" OD2 ASP F 85 " model vdw 2.254 2.440 ... (remaining 110557 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' and resid 38 through 134) selection = chain 'E' } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 20 through 101) } ncs_group { reference = chain 'C' selection = chain 'G' } 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=0.00 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: 4.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 15.270 Check model and map are aligned: 0.180 Set scattering table: 0.140 Process input model: 41.630 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.060 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:11.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 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 0.048 13673 Z= 0.296 Angle : 0.772 8.793 19721 Z= 0.458 Chirality : 0.051 0.521 2229 Planarity : 0.006 0.119 1477 Dihedral : 29.822 177.176 5877 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 0.14 % Allowed : 20.20 % Favored : 79.66 % 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: 0.99 (0.29), residues: 831 helix: 1.68 (0.22), residues: 548 sheet: -2.59 (0.96), residues: 23 loop : -1.27 (0.34), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP K 82 HIS 0.007 0.001 HIS C 82 PHE 0.014 0.002 PHE K 5 TYR 0.013 0.002 TYR F 51 ARG 0.014 0.001 ARG B 35 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 166 time to evaluate : 1.091 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 167 average time/residue: 1.8612 time to fit residues: 328.4049 Evaluate side-chains 113 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 113 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 5.9990 chunk 81 optimal weight: 4.9990 chunk 45 optimal weight: 8.9990 chunk 27 optimal weight: 0.8980 chunk 55 optimal weight: 3.9990 chunk 43 optimal weight: 0.7980 chunk 84 optimal weight: 2.9990 chunk 32 optimal weight: 0.1980 chunk 51 optimal weight: 0.3980 chunk 63 optimal weight: 0.9980 chunk 98 optimal weight: 4.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 46 HIS H 92 GLN K 20 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.1919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 13673 Z= 0.200 Angle : 0.585 10.560 19721 Z= 0.350 Chirality : 0.035 0.137 2229 Planarity : 0.005 0.040 1477 Dihedral : 31.123 177.976 4163 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.10 % Allowed : 21.60 % Favored : 76.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.29), residues: 831 helix: 1.98 (0.22), residues: 555 sheet: -1.66 (1.15), residues: 21 loop : -0.91 (0.35), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP K 21 HIS 0.002 0.001 HIS D 46 PHE 0.011 0.001 PHE K 5 TYR 0.009 0.001 TYR K 68 ARG 0.007 0.000 ARG D 83 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 125 time to evaluate : 1.065 Fit side-chains revert: symmetry clash REVERT: E 97 GLU cc_start: 0.8555 (OUTLIER) cc_final: 0.8199 (mp0) REVERT: E 120 MET cc_start: 0.8817 (OUTLIER) cc_final: 0.8204 (mtt) outliers start: 15 outliers final: 5 residues processed: 131 average time/residue: 1.7891 time to fit residues: 248.8882 Evaluate side-chains 122 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 115 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 77 ASP Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain F residue 24 ASP Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain K residue 25 VAL Chi-restraints excluded: chain K residue 58 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 54 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 81 optimal weight: 4.9990 chunk 66 optimal weight: 0.7980 chunk 27 optimal weight: 0.7980 chunk 98 optimal weight: 4.9990 chunk 106 optimal weight: 3.9990 chunk 87 optimal weight: 3.9990 chunk 97 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN D 44 GLN G 104 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8757 moved from start: 0.2874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 13673 Z= 0.357 Angle : 0.634 10.223 19721 Z= 0.375 Chirality : 0.040 0.152 2229 Planarity : 0.005 0.041 1477 Dihedral : 31.246 176.042 4163 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.66 % Allowed : 21.18 % Favored : 76.16 % 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: 1.41 (0.28), residues: 831 helix: 1.81 (0.22), residues: 551 sheet: -1.66 (1.17), residues: 21 loop : -0.74 (0.34), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP K 21 HIS 0.003 0.001 HIS G 82 PHE 0.010 0.002 PHE E 104 TYR 0.010 0.002 TYR F 51 ARG 0.005 0.001 ARG H 83 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 118 time to evaluate : 1.060 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.9039 (OUTLIER) cc_final: 0.8712 (mtt) REVERT: E 120 MET cc_start: 0.8900 (OUTLIER) cc_final: 0.8347 (mtt) REVERT: K 58 ILE cc_start: 0.5876 (OUTLIER) cc_final: 0.5655 (mt) outliers start: 19 outliers final: 7 residues processed: 129 average time/residue: 1.7158 time to fit residues: 235.1224 Evaluate side-chains 123 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 113 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain H residue 113 LYS Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain K residue 25 VAL Chi-restraints excluded: chain K residue 58 ILE Chi-restraints excluded: chain K residue 90 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 97 optimal weight: 3.9990 chunk 73 optimal weight: 6.9990 chunk 50 optimal weight: 0.6980 chunk 10 optimal weight: 0.5980 chunk 46 optimal weight: 0.0470 chunk 65 optimal weight: 0.9990 chunk 98 optimal weight: 4.9990 chunk 104 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 93 optimal weight: 0.7980 chunk 28 optimal weight: 0.9990 overall best weight: 0.6280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 81 ASN G 73 ASN G 104 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8680 moved from start: 0.3064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 13673 Z= 0.192 Angle : 0.561 11.029 19721 Z= 0.336 Chirality : 0.034 0.135 2229 Planarity : 0.004 0.041 1477 Dihedral : 30.673 178.174 4163 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.96 % Allowed : 21.74 % Favored : 76.30 % 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: 1.65 (0.29), residues: 831 helix: 1.95 (0.22), residues: 557 sheet: -1.96 (0.98), residues: 21 loop : -0.54 (0.35), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP K 82 HIS 0.001 0.000 HIS B 75 PHE 0.005 0.001 PHE B 61 TYR 0.007 0.001 TYR K 61 ARG 0.006 0.000 ARG H 83 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 124 time to evaluate : 0.959 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 120 MET cc_start: 0.8798 (OUTLIER) cc_final: 0.8217 (mtt) outliers start: 14 outliers final: 6 residues processed: 129 average time/residue: 1.6424 time to fit residues: 225.5501 Evaluate side-chains 124 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 117 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 25 VAL Chi-restraints excluded: chain K residue 58 ILE Chi-restraints excluded: chain K residue 90 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 86 optimal weight: 8.9990 chunk 59 optimal weight: 0.9990 chunk 1 optimal weight: 0.8980 chunk 77 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 89 optimal weight: 4.9990 chunk 72 optimal weight: 5.9990 chunk 0 optimal weight: 4.9990 chunk 53 optimal weight: 6.9990 chunk 93 optimal weight: 0.1980 chunk 26 optimal weight: 0.2980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 73 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8696 moved from start: 0.3220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 13673 Z= 0.215 Angle : 0.564 10.707 19721 Z= 0.336 Chirality : 0.034 0.129 2229 Planarity : 0.004 0.053 1477 Dihedral : 30.628 178.359 4163 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.10 % Allowed : 22.16 % Favored : 75.74 % 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: 1.75 (0.29), residues: 831 helix: 2.00 (0.22), residues: 558 sheet: -2.05 (0.85), residues: 23 loop : -0.43 (0.35), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP K 21 HIS 0.002 0.000 HIS G 82 PHE 0.005 0.001 PHE K 5 TYR 0.007 0.001 TYR D 37 ARG 0.006 0.000 ARG H 83 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 116 time to evaluate : 1.062 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 120 MET cc_start: 0.8797 (OUTLIER) cc_final: 0.8220 (mtt) outliers start: 15 outliers final: 9 residues processed: 122 average time/residue: 1.6955 time to fit residues: 220.4247 Evaluate side-chains 125 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 115 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 25 VAL Chi-restraints excluded: chain K residue 58 ILE Chi-restraints excluded: chain K residue 90 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 35 optimal weight: 0.8980 chunk 94 optimal weight: 4.9990 chunk 20 optimal weight: 0.7980 chunk 61 optimal weight: 0.9990 chunk 25 optimal weight: 3.9990 chunk 104 optimal weight: 2.9990 chunk 86 optimal weight: 4.9990 chunk 48 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 54 optimal weight: 0.0670 overall best weight: 0.7320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8690 moved from start: 0.3256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 13673 Z= 0.199 Angle : 0.561 11.201 19721 Z= 0.334 Chirality : 0.034 0.127 2229 Planarity : 0.004 0.041 1477 Dihedral : 30.603 178.445 4163 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.40 % Allowed : 23.14 % Favored : 75.46 % 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: 1.80 (0.29), residues: 831 helix: 2.04 (0.22), residues: 558 sheet: -2.08 (0.82), residues: 23 loop : -0.39 (0.35), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP K 82 HIS 0.002 0.000 HIS B 75 PHE 0.005 0.001 PHE B 61 TYR 0.011 0.001 TYR K 61 ARG 0.004 0.000 ARG K 74 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 121 time to evaluate : 1.085 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 120 MET cc_start: 0.8791 (OUTLIER) cc_final: 0.8212 (mtt) REVERT: K 83 GLU cc_start: 0.8030 (pt0) cc_final: 0.7819 (pt0) outliers start: 10 outliers final: 8 residues processed: 125 average time/residue: 1.7817 time to fit residues: 237.1529 Evaluate side-chains 125 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 116 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 25 VAL Chi-restraints excluded: chain K residue 58 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 100 optimal weight: 3.9990 chunk 11 optimal weight: 0.8980 chunk 59 optimal weight: 0.3980 chunk 76 optimal weight: 3.9990 chunk 87 optimal weight: 6.9990 chunk 58 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 63 optimal weight: 0.4980 chunk 48 optimal weight: 0.7980 chunk 64 optimal weight: 1.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN ** K 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8679 moved from start: 0.3387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 13673 Z= 0.198 Angle : 0.552 8.150 19721 Z= 0.330 Chirality : 0.034 0.154 2229 Planarity : 0.004 0.041 1477 Dihedral : 30.464 178.858 4163 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.96 % Allowed : 22.58 % Favored : 75.46 % 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: 1.89 (0.29), residues: 831 helix: 2.07 (0.22), residues: 560 sheet: -1.78 (0.81), residues: 23 loop : -0.32 (0.36), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP K 82 HIS 0.002 0.000 HIS B 75 PHE 0.005 0.001 PHE B 61 TYR 0.007 0.001 TYR K 61 ARG 0.004 0.000 ARG G 99 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 111 time to evaluate : 1.037 Fit side-chains revert: symmetry clash REVERT: E 120 MET cc_start: 0.8783 (OUTLIER) cc_final: 0.8200 (mtt) REVERT: K 83 GLU cc_start: 0.8011 (pt0) cc_final: 0.7796 (pt0) outliers start: 14 outliers final: 8 residues processed: 119 average time/residue: 1.6416 time to fit residues: 208.2239 Evaluate side-chains 119 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 110 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 25 VAL Chi-restraints excluded: chain K residue 57 ASP Chi-restraints excluded: chain K residue 58 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 41 optimal weight: 0.5980 chunk 62 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 chunk 20 optimal weight: 0.0980 chunk 66 optimal weight: 0.9980 chunk 70 optimal weight: 0.7980 chunk 51 optimal weight: 4.9990 chunk 9 optimal weight: 5.9990 chunk 81 optimal weight: 4.9990 chunk 94 optimal weight: 4.9990 chunk 99 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 72 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 moved from start: 0.3598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 13673 Z= 0.195 Angle : 0.547 8.525 19721 Z= 0.327 Chirality : 0.033 0.126 2229 Planarity : 0.004 0.041 1477 Dihedral : 30.342 179.255 4163 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.54 % Allowed : 24.26 % Favored : 74.19 % 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: 2.02 (0.29), residues: 831 helix: 2.16 (0.22), residues: 558 sheet: -1.67 (0.83), residues: 23 loop : -0.21 (0.36), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP K 21 HIS 0.002 0.000 HIS B 75 PHE 0.005 0.001 PHE B 61 TYR 0.007 0.001 TYR K 61 ARG 0.004 0.000 ARG G 99 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 122 time to evaluate : 1.016 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 120 MET cc_start: 0.8767 (OUTLIER) cc_final: 0.8175 (mtt) outliers start: 11 outliers final: 5 residues processed: 127 average time/residue: 1.7469 time to fit residues: 235.8127 Evaluate side-chains 121 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 115 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 25 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 90 optimal weight: 4.9990 chunk 97 optimal weight: 3.9990 chunk 99 optimal weight: 4.9990 chunk 58 optimal weight: 4.9990 chunk 42 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 87 optimal weight: 0.6980 chunk 91 optimal weight: 5.9990 chunk 96 optimal weight: 2.9990 chunk 63 optimal weight: 0.6980 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8779 moved from start: 0.3706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.052 13673 Z= 0.413 Angle : 0.651 9.315 19721 Z= 0.379 Chirality : 0.041 0.142 2229 Planarity : 0.005 0.041 1477 Dihedral : 30.724 177.670 4163 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.82 % Allowed : 24.54 % Favored : 73.63 % 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: 1.65 (0.28), residues: 831 helix: 1.95 (0.22), residues: 549 sheet: -2.39 (0.87), residues: 26 loop : -0.36 (0.34), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP K 82 HIS 0.004 0.001 HIS G 82 PHE 0.016 0.002 PHE K 5 TYR 0.011 0.001 TYR H 39 ARG 0.005 0.001 ARG K 3 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 113 time to evaluate : 0.924 Fit side-chains revert: symmetry clash REVERT: E 77 ASP cc_start: 0.8486 (OUTLIER) cc_final: 0.8257 (p0) REVERT: E 120 MET cc_start: 0.8892 (OUTLIER) cc_final: 0.8352 (mtt) outliers start: 13 outliers final: 8 residues processed: 119 average time/residue: 1.7665 time to fit residues: 223.2502 Evaluate side-chains 120 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 110 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain E residue 77 ASP Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain H residue 113 LYS Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 25 VAL Chi-restraints excluded: chain K residue 63 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 102 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 71 optimal weight: 0.9980 chunk 107 optimal weight: 5.9990 chunk 99 optimal weight: 3.9990 chunk 85 optimal weight: 3.9990 chunk 8 optimal weight: 0.9980 chunk 66 optimal weight: 0.6980 chunk 52 optimal weight: 0.9980 chunk 68 optimal weight: 0.8980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 44 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8748 moved from start: 0.3721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 13673 Z= 0.220 Angle : 0.603 9.716 19721 Z= 0.356 Chirality : 0.036 0.145 2229 Planarity : 0.005 0.042 1477 Dihedral : 30.683 177.866 4163 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.40 % Allowed : 24.26 % Favored : 74.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.76 (0.29), residues: 831 helix: 2.02 (0.22), residues: 546 sheet: -2.09 (0.89), residues: 25 loop : -0.29 (0.35), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP K 82 HIS 0.009 0.001 HIS K 20 PHE 0.011 0.001 PHE K 5 TYR 0.008 0.001 TYR B 51 ARG 0.006 0.000 ARG K 74 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 112 time to evaluate : 0.924 Fit side-chains REVERT: E 77 ASP cc_start: 0.8443 (OUTLIER) cc_final: 0.8211 (p0) REVERT: E 120 MET cc_start: 0.8868 (OUTLIER) cc_final: 0.8313 (mtt) outliers start: 10 outliers final: 4 residues processed: 117 average time/residue: 1.7888 time to fit residues: 222.2847 Evaluate side-chains 115 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 109 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain E residue 77 ASP Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain H residue 113 LYS Chi-restraints excluded: chain K residue 25 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 23 optimal weight: 0.0970 chunk 85 optimal weight: 3.9990 chunk 35 optimal weight: 0.8980 chunk 88 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 15 optimal weight: 1.9990 chunk 75 optimal weight: 4.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.072467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.049711 restraints weight = 35461.537| |-----------------------------------------------------------------------------| r_work (start): 0.2849 rms_B_bonded: 1.55 r_work: 0.2692 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2575 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8982 moved from start: 0.3728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 13673 Z= 0.234 Angle : 0.604 9.726 19721 Z= 0.355 Chirality : 0.036 0.137 2229 Planarity : 0.005 0.064 1477 Dihedral : 30.592 178.013 4163 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.12 % Allowed : 24.96 % Favored : 73.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.84 (0.29), residues: 831 helix: 2.06 (0.22), residues: 546 sheet: -2.09 (0.89), residues: 25 loop : -0.20 (0.36), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP K 82 HIS 0.002 0.001 HIS K 20 PHE 0.006 0.001 PHE E 104 TYR 0.007 0.001 TYR H 39 ARG 0.006 0.000 ARG K 74 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4597.30 seconds wall clock time: 81 minutes 30.74 seconds (4890.74 seconds total)