Starting phenix.real_space_refine (version: 1.21rc1) on Fri Jul 7 04:22:42 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ea5_31039/07_2023/7ea5_31039_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ea5_31039/07_2023/7ea5_31039.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ea5_31039/07_2023/7ea5_31039.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ea5_31039/07_2023/7ea5_31039.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ea5_31039/07_2023/7ea5_31039_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ea5_31039/07_2023/7ea5_31039_updated.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.005 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: 6 Type Number sf(0) Gaussians Zn 3 6.06 5 P 290 5.49 5 S 33 5.16 5 C 7743 2.51 5 N 2547 2.21 5 O 3154 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "G ARG 71": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/chem_data/mon_lib" Total number of atoms: 13770 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 830 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 4, 'TRANS': 96} Chain: "B" Number of atoms: 622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 622 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "C" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 809 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "D" Number of atoms: 730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 730 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "E" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 802 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "F" Number of atoms: 622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 622 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "G" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 800 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "H" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 714 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "I" Number of atoms: 2955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2955 Classifications: {'DNA': 145} Link IDs: {'rna3p': 144} Chain: "J" Number of atoms: 2990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2990 Classifications: {'DNA': 145} Link IDs: {'rna3p': 144} Chain: "K" Number of atoms: 1896 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1896 Unusual residues: {' ZN': 3} Classifications: {'peptide': 229, 'undetermined': 3} Link IDs: {'PTRANS': 4, 'TRANS': 223, None: 4} Not linked: pdbres="GLY K 260 " pdbres=" ZN K 301 " Not linked: pdbres=" ZN K 301 " pdbres=" ZN K 302 " Not linked: pdbres=" ZN K 302 " pdbres=" ZN K 303 " Not linked: pdbres=" ZN K 303 " pdbres="SAM K 304 " List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 12277 SG CYS K 82 65.116 67.711 47.853 1.00 53.52 S ATOM 12395 SG CYS K 97 60.815 66.338 50.205 1.00 41.97 S ATOM 12450 SG CYS K 105 64.400 68.875 51.580 1.00 57.96 S ATOM 12168 SG CYS K 68 65.754 65.298 51.958 1.00 49.16 S ATOM 12182 SG CYS K 70 68.099 67.624 50.381 1.00 61.08 S ATOM 12277 SG CYS K 82 65.116 67.711 47.853 1.00 53.52 S ATOM 13648 SG CYS K 248 53.165 52.723 14.294 1.00 68.97 S ATOM 13705 SG CYS K 255 56.658 49.593 12.841 1.00 58.18 S Time building chain proxies: 7.10, per 1000 atoms: 0.52 Number of scatterers: 13770 At special positions: 0 Unit cell: (154.78, 91.56, 130.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 3 29.99 S 33 16.00 P 290 15.00 O 3154 8.00 N 2547 7.00 C 7743 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: 6.67 Conformation dependent library (CDL) restraints added in 1.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN K 301 " pdb="ZN ZN K 301 " - pdb=" SG CYS K 82 " pdb="ZN ZN K 301 " - pdb=" SG CYS K 105 " pdb="ZN ZN K 301 " - pdb=" SG CYS K 97 " pdb=" ZN K 302 " pdb="ZN ZN K 302 " - pdb=" SG CYS K 68 " pdb="ZN ZN K 302 " - pdb=" SG CYS K 82 " pdb="ZN ZN K 302 " - pdb=" SG CYS K 70 " pdb=" ZN K 303 " pdb="ZN ZN K 303 " - pdb=" SG CYS K 255 " pdb="ZN ZN K 303 " - pdb=" SG CYS K 248 " 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1832 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 38 helices and 2 sheets defined 52.0% alpha, 1.2% beta 143 base pairs and 240 stacking pairs defined. Time for finding SS restraints: 5.91 Creating SS restraints... Processing helix chain 'A' and resid 45 through 56 Processing helix chain 'A' and resid 64 through 76 Processing helix chain 'A' and resid 87 through 113 removed outlier: 3.638A pdb=" N ALA A 98 " --> pdb=" O GLU A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 131 Processing helix chain 'B' and resid 25 through 28 Processing helix chain 'B' and resid 31 through 41 removed outlier: 3.534A pdb=" N ARG B 36 " --> pdb=" O PRO B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 75 removed outlier: 3.894A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 92 Processing helix chain 'C' and resid 17 through 21 Processing helix chain 'C' and resid 28 through 36 Processing helix chain 'C' and resid 47 through 72 removed outlier: 3.755A pdb=" N LEU C 65 " --> pdb=" O GLU C 61 " (cutoff:3.500A) 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 80 Processing helix chain 'D' and resid 88 through 98 Processing helix chain 'D' and resid 102 through 119 Processing helix chain 'E' and resid 45 through 56 Processing helix chain 'E' and resid 64 through 75 Processing helix chain 'E' and resid 86 through 113 removed outlier: 3.792A pdb=" N MET E 90 " --> pdb=" O SER E 86 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ASP E 106 " --> pdb=" O ALA E 102 " (cutoff:3.500A) Processing helix chain 'E' and resid 121 through 131 removed outlier: 3.529A pdb=" N ARG E 131 " --> pdb=" O ALA E 127 " (cutoff:3.500A) 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 50 through 75 Processing helix chain 'F' and resid 83 through 93 Processing helix chain 'G' and resid 17 through 21 Processing helix chain 'G' and resid 28 through 36 Processing helix chain 'G' and resid 47 through 73 removed outlier: 4.004A pdb=" N ASN G 73 " --> pdb=" O ALA G 69 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 88 Processing helix chain 'G' and resid 91 through 96 Processing helix chain 'H' and resid 35 through 45 removed outlier: 3.868A pdb=" N TYR H 39 " --> pdb=" O ALA H 35 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLN H 44 " --> pdb=" O LYS H 40 " (cutoff:3.500A) 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 119 removed outlier: 3.761A pdb=" N LYS H 105 " --> pdb=" O GLY H 101 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N HIS H 106 " --> pdb=" O GLU H 102 " (cutoff:3.500A) Processing helix chain 'K' and resid 34 through 43 removed outlier: 3.706A pdb=" N LEU K 41 " --> pdb=" O GLU K 38 " (cutoff:3.500A) Processing helix chain 'K' and resid 89 through 92 No H-bonds generated for 'chain 'K' and resid 89 through 92' Processing helix chain 'K' and resid 156 through 168 removed outlier: 4.152A pdb=" N ASP K 161 " --> pdb=" O MET K 157 " (cutoff:3.500A) Processing helix chain 'K' and resid 193 through 195 No H-bonds generated for 'chain 'K' and resid 193 through 195' Processing sheet with id= A, first strand: chain 'K' and resid 122 through 124 removed outlier: 4.030A pdb=" N ALA K 123 " --> pdb=" O ARG K 135 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'K' and resid 152 through 155 352 hydrogen bonds defined for protein. 1032 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 367 hydrogen bonds 734 hydrogen bond angles 0 basepair planarities 143 basepair parallelities 240 stacking parallelities Total time for adding SS restraints: 5.03 Time building geometry restraints manager: 6.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3042 1.34 - 1.46: 4521 1.46 - 1.58: 6418 1.58 - 1.70: 578 1.70 - 1.82: 51 Bond restraints: 14610 Sorted by residual: bond pdb=" C2 SAM K 304 " pdb=" N3 SAM K 304 " ideal model delta sigma weight residual 1.322 1.382 -0.060 2.00e-02 2.50e+03 8.89e+00 bond pdb=" C8 SAM K 304 " pdb=" N7 SAM K 304 " ideal model delta sigma weight residual 1.298 1.351 -0.053 2.00e-02 2.50e+03 7.08e+00 bond pdb=" C2 SAM K 304 " pdb=" N1 SAM K 304 " ideal model delta sigma weight residual 1.329 1.381 -0.052 2.00e-02 2.50e+03 6.67e+00 bond pdb=" C6 SAM K 304 " pdb=" N1 SAM K 304 " ideal model delta sigma weight residual 1.337 1.379 -0.042 2.00e-02 2.50e+03 4.44e+00 bond pdb=" C3' DA J 19 " pdb=" O3' DA J 19 " ideal model delta sigma weight residual 1.422 1.479 -0.057 3.00e-02 1.11e+03 3.60e+00 ... (remaining 14605 not shown) Histogram of bond angle deviations from ideal: 98.43 - 105.53: 1439 105.53 - 112.63: 7889 112.63 - 119.74: 4824 119.74 - 126.84: 6020 126.84 - 133.94: 795 Bond angle restraints: 20967 Sorted by residual: angle pdb=" C3' DA J 19 " pdb=" O3' DA J 19 " pdb=" P DC J 20 " ideal model delta sigma weight residual 120.20 124.75 -4.55 1.50e+00 4.44e-01 9.20e+00 angle pdb=" N SER D 84 " pdb=" CA SER D 84 " pdb=" C SER D 84 " ideal model delta sigma weight residual 114.56 110.74 3.82 1.27e+00 6.20e-01 9.07e+00 angle pdb=" C GLY C 46 " pdb=" N ALA C 47 " pdb=" CA ALA C 47 " ideal model delta sigma weight residual 119.78 123.45 -3.67 1.24e+00 6.50e-01 8.74e+00 angle pdb=" CA LYS B 31 " pdb=" C LYS B 31 " pdb=" N PRO B 32 " ideal model delta sigma weight residual 118.44 123.01 -4.57 1.59e+00 3.96e-01 8.28e+00 angle pdb=" O SAM K 304 " pdb=" C SAM K 304 " pdb=" OXT SAM K 304 " ideal model delta sigma weight residual 126.77 118.14 8.63 3.00e+00 1.11e-01 8.28e+00 ... (remaining 20962 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.35: 6520 35.35 - 70.70: 1230 70.70 - 106.05: 16 106.05 - 141.41: 3 141.41 - 176.76: 1 Dihedral angle restraints: 7770 sinusoidal: 4930 harmonic: 2840 Sorted by residual: dihedral pdb=" C4' DA J 19 " pdb=" C3' DA J 19 " pdb=" O3' DA J 19 " pdb=" P DC J 20 " ideal model delta sinusoidal sigma weight residual -140.00 36.76 -176.76 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DG J 94 " pdb=" C3' DG J 94 " pdb=" O3' DG J 94 " pdb=" P DG J 95 " ideal model delta sinusoidal sigma weight residual 220.00 81.82 138.18 1 3.50e+01 8.16e-04 1.37e+01 dihedral pdb=" C4' DC J 126 " pdb=" C3' DC J 126 " pdb=" O3' DC J 126 " pdb=" P DC J 127 " ideal model delta sinusoidal sigma weight residual 220.00 82.01 137.99 1 3.50e+01 8.16e-04 1.37e+01 ... (remaining 7767 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1846 0.044 - 0.089: 398 0.089 - 0.133: 97 0.133 - 0.177: 14 0.177 - 0.222: 3 Chirality restraints: 2358 Sorted by residual: chirality pdb=" SD SAM K 304 " pdb=" CG SAM K 304 " pdb=" CE SAM K 304 " pdb=" C5' SAM K 304 " both_signs ideal model delta sigma weight residual False 5.50 5.28 0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" C1' SAM K 304 " pdb=" C2' SAM K 304 " pdb=" N9 SAM K 304 " pdb=" O4' SAM K 304 " both_signs ideal model delta sigma weight residual False 2.30 2.48 -0.19 2.00e-01 2.50e+01 8.57e-01 chirality pdb=" C2' SAM K 304 " pdb=" C1' SAM K 304 " pdb=" C3' SAM K 304 " pdb=" O2' SAM K 304 " both_signs ideal model delta sigma weight residual False -2.76 -2.57 -0.18 2.00e-01 2.50e+01 8.25e-01 ... (remaining 2355 not shown) Planarity restraints: 1663 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU K 252 " -0.039 5.00e-02 4.00e+02 5.88e-02 5.52e+00 pdb=" N PRO K 253 " 0.102 5.00e-02 4.00e+02 pdb=" CA PRO K 253 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO K 253 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 79 " 0.034 5.00e-02 4.00e+02 5.06e-02 4.10e+00 pdb=" N PRO C 80 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO C 80 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO C 80 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE G 79 " 0.032 5.00e-02 4.00e+02 4.83e-02 3.73e+00 pdb=" N PRO G 80 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO G 80 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO G 80 " 0.027 5.00e-02 4.00e+02 ... (remaining 1660 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 3573 2.84 - 3.35: 10841 3.35 - 3.87: 25442 3.87 - 4.38: 29073 4.38 - 4.90: 42196 Nonbonded interactions: 111125 Sorted by model distance: nonbonded pdb=" O ILE K 89 " pdb=" OG1 THR K 93 " model vdw 2.319 2.440 nonbonded pdb=" O CYS K 197 " pdb=" OH TYR K 236 " model vdw 2.320 2.440 nonbonded pdb=" OG1 THR D 29 " pdb=" OP1 DT I 104 " model vdw 2.339 2.440 nonbonded pdb=" NH1 ARG C 42 " pdb=" OG1 THR D 85 " model vdw 2.377 2.520 nonbonded pdb=" OG1 THR A 118 " pdb=" NH1 ARG B 45 " model vdw 2.402 2.520 ... (remaining 111120 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' } ncs_group { reference = (chain 'C' and resid 14 through 117) selection = chain 'G' } ncs_group { reference = (chain 'D' and resid 30 through 120) 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.180 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: 4.350 Check model and map are aligned: 0.220 Set scattering table: 0.140 Process input model: 44.130 Find NCS groups from input model: 0.570 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:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 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 : 0.004 0.060 14610 Z= 0.205 Angle : 0.682 8.630 20967 Z= 0.410 Chirality : 0.041 0.222 2358 Planarity : 0.005 0.059 1663 Dihedral : 24.958 176.756 5938 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 2.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.00 (0.21), residues: 957 helix: -1.43 (0.17), residues: 568 sheet: -2.01 (1.11), residues: 28 loop : -2.78 (0.27), residues: 361 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 279 time to evaluate : 1.058 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 279 average time/residue: 0.4254 time to fit residues: 151.1075 Evaluate side-chains 156 residues out of total 826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 156 time to evaluate : 1.146 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 103 optimal weight: 10.0000 chunk 92 optimal weight: 7.9990 chunk 51 optimal weight: 0.9990 chunk 31 optimal weight: 0.7980 chunk 62 optimal weight: 4.9990 chunk 49 optimal weight: 0.8980 chunk 95 optimal weight: 6.9990 chunk 37 optimal weight: 0.9990 chunk 58 optimal weight: 0.9990 chunk 71 optimal weight: 10.0000 chunk 110 optimal weight: 9.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS A 68 GLN A 125 GLN C 68 ASN D 106 HIS E 39 HIS E 68 GLN F 25 ASN G 38 ASN G 84 GLN H 46 HIS ** K 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.2190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 14610 Z= 0.179 Angle : 0.514 6.480 20967 Z= 0.305 Chirality : 0.033 0.155 2358 Planarity : 0.004 0.040 1663 Dihedral : 29.642 179.924 3996 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer Outliers : 1.57 % 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: -0.62 (0.27), residues: 957 helix: 0.89 (0.22), residues: 567 sheet: -1.54 (1.16), residues: 28 loop : -2.51 (0.27), residues: 362 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 176 time to evaluate : 1.222 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 5 residues processed: 184 average time/residue: 0.3390 time to fit residues: 83.5080 Evaluate side-chains 158 residues out of total 826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 153 time to evaluate : 1.143 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1192 time to fit residues: 2.4717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 61 optimal weight: 3.9990 chunk 34 optimal weight: 0.8980 chunk 92 optimal weight: 6.9990 chunk 75 optimal weight: 6.9990 chunk 30 optimal weight: 0.7980 chunk 110 optimal weight: 6.9990 chunk 119 optimal weight: 4.9990 chunk 98 optimal weight: 10.0000 chunk 37 optimal weight: 0.9990 chunk 89 optimal weight: 8.9990 chunk 109 optimal weight: 6.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 39 HIS E 68 GLN G 31 HIS G 73 ASN K 79 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.3337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.045 14610 Z= 0.293 Angle : 0.586 6.637 20967 Z= 0.342 Chirality : 0.037 0.145 2358 Planarity : 0.005 0.042 1663 Dihedral : 30.032 179.107 3996 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer Outliers : 1.57 % 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: -0.25 (0.27), residues: 957 helix: 1.25 (0.22), residues: 562 sheet: -1.27 (1.18), residues: 28 loop : -2.44 (0.27), residues: 367 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 171 time to evaluate : 1.134 Fit side-chains outliers start: 13 outliers final: 9 residues processed: 176 average time/residue: 0.3880 time to fit residues: 88.9908 Evaluate side-chains 157 residues out of total 826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 148 time to evaluate : 1.133 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1169 time to fit residues: 3.3852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 83 optimal weight: 10.0000 chunk 57 optimal weight: 4.9990 chunk 12 optimal weight: 0.8980 chunk 52 optimal weight: 9.9990 chunk 74 optimal weight: 7.9990 chunk 111 optimal weight: 7.9990 chunk 117 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 105 optimal weight: 6.9990 chunk 31 optimal weight: 0.9980 chunk 98 optimal weight: 10.0000 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 31 HIS E 39 HIS F 25 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.3729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.045 14610 Z= 0.292 Angle : 0.568 6.969 20967 Z= 0.333 Chirality : 0.036 0.144 2358 Planarity : 0.004 0.044 1663 Dihedral : 30.014 178.781 3996 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer Outliers : 1.57 % 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: -0.11 (0.27), residues: 957 helix: 1.35 (0.22), residues: 561 sheet: -1.79 (0.83), residues: 48 loop : -2.27 (0.29), residues: 348 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 148 time to evaluate : 1.217 Fit side-chains outliers start: 13 outliers final: 9 residues processed: 157 average time/residue: 0.3593 time to fit residues: 74.8530 Evaluate side-chains 155 residues out of total 826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 146 time to evaluate : 1.157 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1210 time to fit residues: 3.4454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 66 optimal weight: 0.9990 chunk 1 optimal weight: 0.6980 chunk 87 optimal weight: 10.0000 chunk 48 optimal weight: 0.9990 chunk 100 optimal weight: 6.9990 chunk 81 optimal weight: 7.9990 chunk 0 optimal weight: 7.9990 chunk 60 optimal weight: 3.9990 chunk 105 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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: 0.7987 moved from start: 0.3730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.038 14610 Z= 0.200 Angle : 0.538 6.666 20967 Z= 0.319 Chirality : 0.034 0.136 2358 Planarity : 0.004 0.041 1663 Dihedral : 29.991 178.702 3996 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer Outliers : 0.12 % 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: 0.23 (0.28), residues: 957 helix: 1.63 (0.23), residues: 559 sheet: -1.61 (0.84), residues: 48 loop : -2.13 (0.29), residues: 350 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 157 time to evaluate : 1.076 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 157 average time/residue: 0.3515 time to fit residues: 73.6624 Evaluate side-chains 147 residues out of total 826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 146 time to evaluate : 1.068 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1172 time to fit residues: 1.5229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 106 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 69 optimal weight: 0.0050 chunk 29 optimal weight: 5.9990 chunk 118 optimal weight: 9.9990 chunk 97 optimal weight: 10.0000 chunk 54 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 113 optimal weight: 5.9990 overall best weight: 2.2002 ------------------------------------------------------------------------------- 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: 0.8016 moved from start: 0.3960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.041 14610 Z= 0.275 Angle : 0.561 6.489 20967 Z= 0.330 Chirality : 0.036 0.144 2358 Planarity : 0.004 0.042 1663 Dihedral : 29.972 178.928 3996 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer Outliers : 1.57 % 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: 0.24 (0.28), residues: 957 helix: 1.56 (0.22), residues: 561 sheet: -1.55 (0.85), residues: 48 loop : -2.02 (0.30), residues: 348 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 146 time to evaluate : 1.083 Fit side-chains revert: symmetry clash outliers start: 13 outliers final: 8 residues processed: 153 average time/residue: 0.3711 time to fit residues: 75.1799 Evaluate side-chains 151 residues out of total 826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 143 time to evaluate : 1.177 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1175 time to fit residues: 3.1742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 13 optimal weight: 0.9990 chunk 67 optimal weight: 3.9990 chunk 86 optimal weight: 10.0000 chunk 66 optimal weight: 0.8980 chunk 99 optimal weight: 6.9990 chunk 65 optimal weight: 0.6980 chunk 117 optimal weight: 9.9990 chunk 73 optimal weight: 10.0000 chunk 71 optimal weight: 10.0000 chunk 54 optimal weight: 0.7980 chunk 72 optimal weight: 10.0000 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.3964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.036 14610 Z= 0.213 Angle : 0.541 6.698 20967 Z= 0.320 Chirality : 0.034 0.139 2358 Planarity : 0.004 0.045 1663 Dihedral : 29.922 178.253 3996 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer Outliers : 1.33 % 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: 0.48 (0.28), residues: 957 helix: 1.76 (0.23), residues: 561 sheet: -1.48 (0.85), residues: 48 loop : -1.91 (0.31), residues: 348 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 147 time to evaluate : 1.197 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 8 residues processed: 152 average time/residue: 0.3708 time to fit residues: 74.4509 Evaluate side-chains 150 residues out of total 826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 142 time to evaluate : 1.145 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1653 time to fit residues: 3.5424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 46 optimal weight: 5.9990 chunk 70 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 22 optimal weight: 0.6980 chunk 74 optimal weight: 7.9990 chunk 80 optimal weight: 7.9990 chunk 58 optimal weight: 2.9990 chunk 10 optimal weight: 0.3980 chunk 92 optimal weight: 7.9990 chunk 106 optimal weight: 5.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- 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: 0.7994 moved from start: 0.4011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.048 14610 Z= 0.224 Angle : 0.542 10.488 20967 Z= 0.320 Chirality : 0.034 0.145 2358 Planarity : 0.004 0.044 1663 Dihedral : 29.871 178.285 3996 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer Outliers : 0.73 % 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: 0.59 (0.28), residues: 957 helix: 1.85 (0.23), residues: 560 sheet: -1.40 (1.02), residues: 38 loop : -1.87 (0.30), residues: 359 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 150 time to evaluate : 1.181 Fit side-chains outliers start: 6 outliers final: 5 residues processed: 155 average time/residue: 0.3398 time to fit residues: 71.0861 Evaluate side-chains 149 residues out of total 826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 144 time to evaluate : 1.121 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1275 time to fit residues: 2.5119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 112 optimal weight: 6.9990 chunk 102 optimal weight: 5.9990 chunk 109 optimal weight: 20.0000 chunk 65 optimal weight: 2.9990 chunk 47 optimal weight: 0.7980 chunk 86 optimal weight: 10.0000 chunk 33 optimal weight: 0.6980 chunk 99 optimal weight: 7.9990 chunk 103 optimal weight: 5.9990 chunk 71 optimal weight: 10.0000 chunk 115 optimal weight: 5.9990 overall best weight: 3.2986 ------------------------------------------------------------------------------- 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: 0.8058 moved from start: 0.4359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.051 14610 Z= 0.378 Angle : 0.628 11.863 20967 Z= 0.361 Chirality : 0.039 0.142 2358 Planarity : 0.005 0.052 1663 Dihedral : 30.071 179.857 3996 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer Outliers : 0.61 % 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: 0.11 (0.28), residues: 957 helix: 1.41 (0.22), residues: 560 sheet: -1.32 (0.92), residues: 38 loop : -2.01 (0.30), residues: 359 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 143 time to evaluate : 1.232 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 145 average time/residue: 0.3694 time to fit residues: 71.1199 Evaluate side-chains 136 residues out of total 826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 133 time to evaluate : 1.135 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1161 time to fit residues: 2.0197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 70 optimal weight: 3.9990 chunk 54 optimal weight: 0.8980 chunk 80 optimal weight: 7.9990 chunk 121 optimal weight: 50.0000 chunk 111 optimal weight: 4.9990 chunk 96 optimal weight: 6.9990 chunk 10 optimal weight: 0.9980 chunk 74 optimal weight: 6.9990 chunk 59 optimal weight: 0.1980 chunk 76 optimal weight: 6.9990 chunk 103 optimal weight: 20.0000 overall best weight: 2.2184 ------------------------------------------------------------------------------- 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: 0.8027 moved from start: 0.4345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.046 14610 Z= 0.278 Angle : 0.585 12.602 20967 Z= 0.340 Chirality : 0.036 0.152 2358 Planarity : 0.004 0.042 1663 Dihedral : 29.975 178.323 3996 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer Outliers : 0.00 % 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: 0.27 (0.28), residues: 957 helix: 1.56 (0.22), residues: 558 sheet: -1.37 (0.95), residues: 38 loop : -1.95 (0.30), residues: 361 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 150 time to evaluate : 1.232 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 150 average time/residue: 0.3607 time to fit residues: 72.2466 Evaluate side-chains 144 residues out of total 826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 144 time to evaluate : 1.224 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 29 optimal weight: 3.9990 chunk 89 optimal weight: 8.9990 chunk 14 optimal weight: 0.9990 chunk 26 optimal weight: 0.0030 chunk 96 optimal weight: 6.9990 chunk 40 optimal weight: 3.9990 chunk 99 optimal weight: 9.9990 chunk 12 optimal weight: 0.7980 chunk 17 optimal weight: 7.9990 chunk 85 optimal weight: 20.0000 chunk 5 optimal weight: 1.9990 overall best weight: 1.5596 ------------------------------------------------------------------------------- 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 = 0.3975 r_free = 0.3975 target = 0.173740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.121433 restraints weight = 17290.131| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 2.27 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.4338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.045 14610 Z= 0.221 Angle : 0.575 12.196 20967 Z= 0.335 Chirality : 0.035 0.157 2358 Planarity : 0.004 0.041 1663 Dihedral : 29.969 178.365 3996 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer Outliers : 0.12 % 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: 0.42 (0.28), residues: 957 helix: 1.69 (0.23), residues: 558 sheet: -1.34 (0.96), residues: 38 loop : -1.90 (0.30), residues: 361 =============================================================================== Job complete usr+sys time: 2299.34 seconds wall clock time: 42 minutes 28.85 seconds (2548.85 seconds total)