Starting phenix.real_space_refine on Mon Sep 23 16:42:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7efd_31084/09_2024/7efd_31084.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7efd_31084/09_2024/7efd_31084.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.77 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7efd_31084/09_2024/7efd_31084.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7efd_31084/09_2024/7efd_31084.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7efd_31084/09_2024/7efd_31084.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7efd_31084/09_2024/7efd_31084.cif" } resolution = 1.77 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 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: 4 Type Number sf(0) Gaussians S 4 5.16 5 C 2392 2.51 5 N 668 2.21 5 O 940 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 4004 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 946 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 120, 896 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 1, 'TRANS': 118} Conformer: "B" Number of residues, atoms: 120, 896 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 1, 'TRANS': 118} bond proxies already assigned to first conformer: 867 Chain: "A" Number of atoms: 55 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 40, 55 Unusual residues: {'BTN': 1} Classifications: {'undetermined': 1, 'water': 39} Link IDs: {None: 39} Chain: "B" Number of atoms: 39 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 39, 39 Classifications: {'water': 39} Link IDs: {None: 38} Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 39, 39 Classifications: {'water': 39} Link IDs: {None: 38} Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 39, 39 Classifications: {'water': 39} Link IDs: {None: 38} Restraints were copied for chains: C, B, D Residues with excluded nonbonded symmetry interactions: 56 residue: pdb=" N ASER A 45 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER A 45 " occ=0.50 residue: pdb=" N AALA A 46 " occ=0.50 ... (8 atoms not shown) pdb=" CB BALA A 46 " occ=0.50 residue: pdb=" N AVAL A 47 " occ=0.50 ... (12 atoms not shown) pdb=" CG2BVAL A 47 " occ=0.50 residue: pdb=" N AGLY A 48 " occ=0.50 ... (6 atoms not shown) pdb=" O BGLY A 48 " occ=0.50 residue: pdb=" N AASN A 49 " occ=0.50 ... (14 atoms not shown) pdb=" ND2BASN A 49 " occ=0.50 residue: pdb=" N AALA A 50 " occ=0.50 ... (8 atoms not shown) pdb=" CB BALA A 50 " occ=0.50 residue: pdb=" N AGLU A 51 " occ=0.50 ... (16 atoms not shown) pdb=" OE2BGLU A 51 " occ=0.50 residue: pdb=" N ASER A 52 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER A 52 " occ=0.50 residue: pdb=" C10ABTN A5100 " occ=0.50 ... (14 atoms not shown) pdb=" S1 ABTN A5100 " occ=0.50 residue: pdb=" O HOH A5223 " occ=0.50 residue: pdb=" O AHOH A5225 " occ=0.50 residue: pdb=" O AHOH A5226 " occ=0.50 ... (remaining 44 not shown) Time building chain proxies: 3.12, per 1000 atoms: 0.78 Number of scatterers: 4004 At special positions: 0 Unit cell: (68.8516, 64.4096, 58.4869, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 4 16.00 O 940 8.00 N 668 7.00 C 2392 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.02 Conformation dependent library (CDL) restraints added in 975.3 milliseconds 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 888 Finding SS restraints... Secondary structure from input PDB file: 4 helices and 4 sheets defined 5.8% alpha, 53.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.52 Creating SS restraints... Processing helix chain 'A' and resid 115 through 121 removed outlier: 5.020A pdb=" N TRP A 120 " --> pdb=" O ALA A 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 121 removed outlier: 5.020A pdb=" N TRP B 120 " --> pdb=" O ALA B 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 121 removed outlier: 5.020A pdb=" N TRP C 120 " --> pdb=" O ALA C 117 " (cutoff:3.500A) Processing helix chain 'D' and resid 115 through 121 removed outlier: 5.020A pdb=" N TRP D 120 " --> pdb=" O ALA D 117 " (cutoff:3.500A) Processing sheet with id=1, first strand: chain 'A' and resid 19 through 23 removed outlier: 8.257A pdb=" N ARG A 53 " --> pdb=" O LYS A 80 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N LYS A 80 " --> pdb=" O ARG A 53 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N VAL A 55 " --> pdb=" O ALA A 78 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N ALA A 78 " --> pdb=" O VAL A 55 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N SER A 88 " --> pdb=" O TRP A 79 " (cutoff:3.500A) Processing sheet with id=2, first strand: chain 'B' and resid 19 through 23 removed outlier: 8.257A pdb=" N ARG B 53 " --> pdb=" O LYS B 80 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N LYS B 80 " --> pdb=" O ARG B 53 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N VAL B 55 " --> pdb=" O ALA B 78 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N ALA B 78 " --> pdb=" O VAL B 55 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N SER B 88 " --> pdb=" O TRP B 79 " (cutoff:3.500A) Processing sheet with id=3, first strand: chain 'C' and resid 19 through 23 removed outlier: 8.257A pdb=" N ARG C 53 " --> pdb=" O LYS C 80 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N LYS C 80 " --> pdb=" O ARG C 53 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N VAL C 55 " --> pdb=" O ALA C 78 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N ALA C 78 " --> pdb=" O VAL C 55 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N SER C 88 " --> pdb=" O TRP C 79 " (cutoff:3.500A) Processing sheet with id=4, first strand: chain 'D' and resid 19 through 23 removed outlier: 8.257A pdb=" N ARG D 53 " --> pdb=" O LYS D 80 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N LYS D 80 " --> pdb=" O ARG D 53 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N VAL D 55 " --> pdb=" O ALA D 78 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N ALA D 78 " --> pdb=" O VAL D 55 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N SER D 88 " --> pdb=" O TRP D 79 " (cutoff:3.500A) 208 hydrogen bonds defined for protein. 540 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.28 Time building geometry restraints manager: 1.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.28: 540 1.28 - 1.42: 876 1.42 - 1.55: 2196 1.55 - 1.68: 324 1.68 - 1.82: 8 Bond restraints: 3944 Sorted by residual: bond pdb=" C THR A 42 " pdb=" O THR A 42 " ideal model delta sigma weight residual 1.235 1.353 -0.119 1.22e-02 6.72e+03 9.44e+01 bond pdb=" C THR B 42 " pdb=" O THR B 42 " ideal model delta sigma weight residual 1.235 1.353 -0.119 1.22e-02 6.72e+03 9.44e+01 bond pdb=" C THR D 42 " pdb=" O THR D 42 " ideal model delta sigma weight residual 1.235 1.353 -0.119 1.22e-02 6.72e+03 9.44e+01 bond pdb=" C THR C 42 " pdb=" O THR C 42 " ideal model delta sigma weight residual 1.235 1.353 -0.119 1.22e-02 6.72e+03 9.44e+01 bond pdb=" C GLY D 94 " pdb=" O GLY D 94 " ideal model delta sigma weight residual 1.232 1.313 -0.082 1.05e-02 9.07e+03 6.03e+01 ... (remaining 3939 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.76: 3452 2.76 - 5.51: 1456 5.51 - 8.26: 432 8.26 - 11.01: 40 11.01 - 13.77: 20 Bond angle restraints: 5400 Sorted by residual: angle pdb=" CA PHE A 29 " pdb=" CB PHE A 29 " pdb=" CG PHE A 29 " ideal model delta sigma weight residual 113.80 124.75 -10.95 1.00e+00 1.00e+00 1.20e+02 angle pdb=" CA PHE C 29 " pdb=" CB PHE C 29 " pdb=" CG PHE C 29 " ideal model delta sigma weight residual 113.80 124.75 -10.95 1.00e+00 1.00e+00 1.20e+02 angle pdb=" CA PHE B 29 " pdb=" CB PHE B 29 " pdb=" CG PHE B 29 " ideal model delta sigma weight residual 113.80 124.75 -10.95 1.00e+00 1.00e+00 1.20e+02 angle pdb=" CA PHE D 29 " pdb=" CB PHE D 29 " pdb=" CG PHE D 29 " ideal model delta sigma weight residual 113.80 124.75 -10.95 1.00e+00 1.00e+00 1.20e+02 angle pdb=" CA ILE A 17 " pdb=" C ILE A 17 " pdb=" O ILE A 17 " ideal model delta sigma weight residual 120.85 110.32 10.53 1.06e+00 8.90e-01 9.87e+01 ... (remaining 5395 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 16.60: 2012 16.60 - 33.19: 148 33.19 - 49.79: 28 49.79 - 66.38: 12 66.38 - 82.98: 12 Dihedral angle restraints: 2212 sinusoidal: 788 harmonic: 1424 Sorted by residual: dihedral pdb=" CA ASER C 52 " pdb=" C ASER C 52 " pdb=" N ARG C 53 " pdb=" CA ARG C 53 " ideal model delta harmonic sigma weight residual -180.00 -152.21 -27.79 0 5.00e+00 4.00e-02 3.09e+01 dihedral pdb=" CA ASER B 52 " pdb=" C ASER B 52 " pdb=" N ARG B 53 " pdb=" CA ARG B 53 " ideal model delta harmonic sigma weight residual -180.00 -152.21 -27.79 0 5.00e+00 4.00e-02 3.09e+01 dihedral pdb=" CA ASER D 52 " pdb=" C ASER D 52 " pdb=" N ARG D 53 " pdb=" CA ARG D 53 " ideal model delta harmonic sigma weight residual -180.00 -152.21 -27.79 0 5.00e+00 4.00e-02 3.09e+01 ... (remaining 2209 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 424 0.083 - 0.166: 152 0.166 - 0.248: 20 0.248 - 0.331: 0 0.331 - 0.414: 8 Chirality restraints: 604 Sorted by residual: chirality pdb=" CB VAL D 125 " pdb=" CA VAL D 125 " pdb=" CG1 VAL D 125 " pdb=" CG2 VAL D 125 " both_signs ideal model delta sigma weight residual False -2.63 -2.22 -0.41 2.00e-01 2.50e+01 4.28e+00 chirality pdb=" CB VAL A 125 " pdb=" CA VAL A 125 " pdb=" CG1 VAL A 125 " pdb=" CG2 VAL A 125 " both_signs ideal model delta sigma weight residual False -2.63 -2.22 -0.41 2.00e-01 2.50e+01 4.28e+00 chirality pdb=" CB VAL C 125 " pdb=" CA VAL C 125 " pdb=" CG1 VAL C 125 " pdb=" CG2 VAL C 125 " both_signs ideal model delta sigma weight residual False -2.63 -2.22 -0.41 2.00e-01 2.50e+01 4.28e+00 ... (remaining 601 not shown) Planarity restraints: 684 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C3 ABTN D5100 " 0.059 2.00e-02 2.50e+03 2.01e-01 6.08e+02 pdb=" C4 ABTN D5100 " -0.164 2.00e-02 2.50e+03 pdb=" C5 ABTN D5100 " -0.156 2.00e-02 2.50e+03 pdb=" N1 ABTN D5100 " 0.250 2.00e-02 2.50e+03 pdb=" N2 ABTN D5100 " 0.257 2.00e-02 2.50e+03 pdb=" O3 ABTN D5100 " -0.245 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C3 ABTN B5100 " 0.059 2.00e-02 2.50e+03 2.01e-01 6.08e+02 pdb=" C4 ABTN B5100 " -0.164 2.00e-02 2.50e+03 pdb=" C5 ABTN B5100 " -0.156 2.00e-02 2.50e+03 pdb=" N1 ABTN B5100 " 0.250 2.00e-02 2.50e+03 pdb=" N2 ABTN B5100 " 0.257 2.00e-02 2.50e+03 pdb=" O3 ABTN B5100 " -0.245 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C3 ABTN A5100 " -0.059 2.00e-02 2.50e+03 2.01e-01 6.08e+02 pdb=" C4 ABTN A5100 " 0.164 2.00e-02 2.50e+03 pdb=" C5 ABTN A5100 " 0.156 2.00e-02 2.50e+03 pdb=" N1 ABTN A5100 " -0.250 2.00e-02 2.50e+03 pdb=" N2 ABTN A5100 " -0.257 2.00e-02 2.50e+03 pdb=" O3 ABTN A5100 " 0.245 2.00e-02 2.50e+03 ... (remaining 681 not shown) Histogram of nonbonded interaction distances: 0.00 - 0.98: 2 0.98 - 1.96: 0 1.96 - 2.94: 1410 2.94 - 3.92: 11570 3.92 - 4.90: 22800 Warning: very small nonbonded interaction distances. Nonbonded interactions: 35782 Sorted by model distance: nonbonded pdb=" O HOH A5223 " pdb=" O HOH C5223 " model vdw 0.001 3.040 nonbonded pdb=" O HOH B5223 " pdb=" O HOH D5223 " model vdw 0.001 3.040 nonbonded pdb=" O AASN A 49 " pdb=" OD1AASN A 49 " model vdw 2.212 3.040 nonbonded pdb=" O AASN B 49 " pdb=" OD1AASN B 49 " model vdw 2.212 3.040 nonbonded pdb=" O AASN D 49 " pdb=" OD1AASN D 49 " model vdw 2.212 3.040 ... (remaining 35777 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 15 through 44 or resid 53 through 134 or resid 5100)) selection = (chain 'B' and (resid 15 through 44 or resid 53 through 134 or resid 5100)) selection = (chain 'C' and (resid 15 through 44 or resid 53 through 134 or resid 5100)) selection = (chain 'D' and (resid 15 through 44 or resid 53 through 134 or resid 5100)) } 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=0.50 max=1.00 mean=0.94 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: 0.190 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: 0.180 Check model and map are aligned: 0.020 Set scattering table: 0.050 Process input model: 15.690 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.020 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:12.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 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 : 0.033 0.119 3944 Z= 2.153 Angle : 3.163 13.767 5400 Z= 2.200 Chirality : 0.091 0.414 604 Planarity : 0.015 0.201 684 Dihedral : 15.318 82.977 1324 Min Nonbonded Distance : 0.001 Molprobity Statistics. All-atom Clashscore : 1.61 Ramachandran Plot: Outliers : 0.85 % Allowed : 1.69 % Favored : 97.46 % Rotamer: Outliers : 2.15 % Allowed : 4.30 % Favored : 93.55 % Cbeta Deviations : 2.70 % 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: -0.54 (0.34), residues: 512 helix: None (None), residues: 0 sheet: 0.53 (0.31), residues: 224 loop : -1.12 (0.33), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 92 HIS 0.001 0.000 HIS B 127 PHE 0.002 0.001 PHE C 130 TYR 0.002 0.001 TYR D 60 ARG 0.000 0.000 ARG A 103 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 64 time to evaluate : 0.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 SER cc_start: 0.8196 (m) cc_final: 0.7701 (p) REVERT: A 103 ARG cc_start: 0.8211 (ttm-80) cc_final: 0.7454 (ttp80) REVERT: B 27 SER cc_start: 0.8197 (m) cc_final: 0.7701 (p) REVERT: B 103 ARG cc_start: 0.8210 (ttm-80) cc_final: 0.7455 (ttp80) REVERT: C 27 SER cc_start: 0.8195 (m) cc_final: 0.7701 (p) REVERT: C 103 ARG cc_start: 0.8210 (ttm-80) cc_final: 0.7454 (ttp80) REVERT: D 27 SER cc_start: 0.8197 (m) cc_final: 0.7702 (p) REVERT: D 103 ARG cc_start: 0.8211 (ttm-80) cc_final: 0.7454 (ttp80) outliers start: 8 outliers final: 4 residues processed: 64 average time/residue: 1.4566 time to fit residues: 95.8986 Evaluate side-chains 60 residues out of total 332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 56 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain D residue 28 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 40 optimal weight: 7.9990 chunk 36 optimal weight: 5.9990 chunk 20 optimal weight: 8.9990 chunk 12 optimal weight: 5.9990 chunk 24 optimal weight: 5.9990 chunk 19 optimal weight: 20.0000 chunk 37 optimal weight: 5.9990 chunk 14 optimal weight: 5.9990 chunk 22 optimal weight: 6.9990 chunk 28 optimal weight: 6.9990 chunk 43 optimal weight: 9.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 GLN A 118 ASN B 107 GLN B 118 ASN C 107 GLN C 118 ASN D 107 GLN D 118 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.1658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.162 3944 Z= 0.722 Angle : 1.700 22.900 5400 Z= 0.930 Chirality : 0.081 0.397 604 Planarity : 0.021 0.380 684 Dihedral : 9.903 59.927 636 Min Nonbonded Distance : 1.751 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.85 % Allowed : 2.75 % Favored : 96.40 % Rotamer: Outliers : 2.15 % Allowed : 10.48 % Favored : 87.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -1.32 (0.34), residues: 512 helix: -4.64 (0.24), residues: 24 sheet: 0.02 (0.27), residues: 264 loop : -1.49 (0.40), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.077 0.009 TRP B 108 HIS 0.008 0.003 HIS C 87 PHE 0.119 0.019 PHE B 29 TYR 0.284 0.016 TYR C 43 ARG 0.157 0.010 ARG C 53 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 63 time to evaluate : 0.397 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 SER cc_start: 0.8199 (m) cc_final: 0.7835 (p) REVERT: A 103 ARG cc_start: 0.8072 (ttm-80) cc_final: 0.7424 (ttm110) REVERT: B 27 SER cc_start: 0.8155 (m) cc_final: 0.7796 (p) REVERT: B 53 ARG cc_start: 0.7672 (ttp80) cc_final: 0.7252 (mtm-85) REVERT: C 27 SER cc_start: 0.8187 (m) cc_final: 0.7838 (p) REVERT: C 53 ARG cc_start: 0.7721 (ttp80) cc_final: 0.7469 (ttm170) REVERT: C 103 ARG cc_start: 0.8060 (ttm-80) cc_final: 0.7435 (ttp80) REVERT: D 27 SER cc_start: 0.8194 (m) cc_final: 0.7863 (p) outliers start: 8 outliers final: 0 residues processed: 68 average time/residue: 1.2958 time to fit residues: 90.8612 Evaluate side-chains 56 residues out of total 332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 56 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 24 optimal weight: 5.9990 chunk 13 optimal weight: 5.9990 chunk 36 optimal weight: 7.9990 chunk 29 optimal weight: 0.9990 chunk 12 optimal weight: 5.9990 chunk 43 optimal weight: 0.8980 chunk 47 optimal weight: 6.9990 chunk 38 optimal weight: 0.9990 chunk 14 optimal weight: 6.9990 chunk 35 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 107 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.2388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3944 Z= 0.170 Angle : 0.680 9.019 5400 Z= 0.363 Chirality : 0.042 0.137 604 Planarity : 0.003 0.025 684 Dihedral : 7.181 49.875 632 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.85 % Allowed : 2.54 % Favored : 96.61 % Rotamer: Outliers : 0.00 % Allowed : 9.68 % Favored : 90.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.38), residues: 512 helix: None (None), residues: 0 sheet: 0.15 (0.25), residues: 316 loop : 0.73 (0.55), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 75 HIS 0.003 0.001 HIS C 87 PHE 0.016 0.003 PHE D 29 TYR 0.012 0.002 TYR B 22 ARG 0.002 0.000 ARG A 103 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 71 time to evaluate : 0.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 ARG cc_start: 0.8092 (ttm-80) cc_final: 0.7477 (ttm110) REVERT: B 27 SER cc_start: 0.8113 (m) cc_final: 0.7694 (p) REVERT: B 103 ARG cc_start: 0.8161 (ttm-80) cc_final: 0.7417 (ttp80) REVERT: B 107 GLN cc_start: 0.8292 (mt0) cc_final: 0.8087 (mt0) REVERT: C 27 SER cc_start: 0.8200 (m) cc_final: 0.7793 (p) REVERT: C 103 ARG cc_start: 0.8092 (ttm-80) cc_final: 0.7487 (ttm110) REVERT: D 103 ARG cc_start: 0.8228 (ttm-80) cc_final: 0.7496 (ttm110) outliers start: 0 outliers final: 0 residues processed: 71 average time/residue: 1.3323 time to fit residues: 97.4813 Evaluate side-chains 68 residues out of total 332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 68 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 22 optimal weight: 0.9980 chunk 4 optimal weight: 6.9990 chunk 20 optimal weight: 2.9990 chunk 29 optimal weight: 0.8980 chunk 43 optimal weight: 20.0000 chunk 46 optimal weight: 5.9990 chunk 41 optimal weight: 0.7980 chunk 12 optimal weight: 20.0000 chunk 38 optimal weight: 9.9990 chunk 26 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 overall best weight: 2.3384 ------------------------------------------------------------------------------- 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: 0.8074 moved from start: 0.2686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3944 Z= 0.197 Angle : 0.669 7.921 5400 Z= 0.362 Chirality : 0.044 0.155 604 Planarity : 0.003 0.020 684 Dihedral : 6.840 43.573 632 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.64 % Allowed : 2.97 % Favored : 96.40 % Rotamer: Outliers : 0.27 % Allowed : 10.75 % Favored : 88.98 % 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: 0.60 (0.38), residues: 512 helix: None (None), residues: 0 sheet: 0.38 (0.26), residues: 312 loop : 0.68 (0.54), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 92 HIS 0.003 0.001 HIS C 87 PHE 0.018 0.003 PHE B 29 TYR 0.011 0.002 TYR B 22 ARG 0.002 0.000 ARG A 103 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 71 time to evaluate : 0.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 ARG cc_start: 0.8040 (ttm-80) cc_final: 0.7480 (ttm110) REVERT: B 103 ARG cc_start: 0.8174 (ttm-80) cc_final: 0.7428 (ttp80) REVERT: C 27 SER cc_start: 0.8210 (m) cc_final: 0.7974 (m) REVERT: C 103 ARG cc_start: 0.8030 (ttm-80) cc_final: 0.7465 (ttm110) REVERT: D 103 ARG cc_start: 0.8211 (ttm-80) cc_final: 0.7515 (ttm110) outliers start: 1 outliers final: 0 residues processed: 71 average time/residue: 1.3276 time to fit residues: 97.2148 Evaluate side-chains 65 residues out of total 332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 65 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 34 optimal weight: 5.9990 chunk 19 optimal weight: 20.0000 chunk 39 optimal weight: 0.1980 chunk 32 optimal weight: 8.9990 chunk 0 optimal weight: 20.0000 chunk 23 optimal weight: 5.9990 chunk 41 optimal weight: 0.0470 chunk 11 optimal weight: 9.9990 chunk 15 optimal weight: 20.0000 chunk 9 optimal weight: 0.9980 chunk 27 optimal weight: 10.0000 overall best weight: 2.6482 ------------------------------------------------------------------------------- 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: 0.8077 moved from start: 0.2828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3944 Z= 0.208 Angle : 0.653 7.010 5400 Z= 0.357 Chirality : 0.044 0.153 604 Planarity : 0.003 0.017 684 Dihedral : 6.883 44.434 632 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 0.27 % Allowed : 11.56 % Favored : 88.17 % 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: 0.78 (0.38), residues: 512 helix: None (None), residues: 0 sheet: 0.48 (0.26), residues: 308 loop : 0.83 (0.52), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 92 HIS 0.003 0.001 HIS C 87 PHE 0.013 0.002 PHE B 29 TYR 0.011 0.002 TYR A 22 ARG 0.003 0.000 ARG A 103 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 71 time to evaluate : 0.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 ARG cc_start: 0.8041 (ttm-80) cc_final: 0.7515 (ttm110) REVERT: B 103 ARG cc_start: 0.8152 (ttm-80) cc_final: 0.7421 (ttp80) REVERT: C 27 SER cc_start: 0.8162 (m) cc_final: 0.7913 (m) REVERT: C 103 ARG cc_start: 0.8045 (ttm-80) cc_final: 0.7535 (ttm110) REVERT: D 103 ARG cc_start: 0.8195 (ttm-80) cc_final: 0.7533 (ttm110) outliers start: 1 outliers final: 0 residues processed: 71 average time/residue: 1.3905 time to fit residues: 101.6151 Evaluate side-chains 71 residues out of total 332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 71 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 11 optimal weight: 9.9990 chunk 46 optimal weight: 10.0000 chunk 38 optimal weight: 20.0000 chunk 21 optimal weight: 8.9990 chunk 3 optimal weight: 8.9990 chunk 15 optimal weight: 20.0000 chunk 24 optimal weight: 20.0000 chunk 44 optimal weight: 4.9990 chunk 5 optimal weight: 0.9990 chunk 26 optimal weight: 9.9990 chunk 33 optimal weight: 20.0000 overall best weight: 6.7990 ------------------------------------------------------------------------------- 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: 0.8099 moved from start: 0.2999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 3944 Z= 0.410 Angle : 0.809 5.306 5400 Z= 0.452 Chirality : 0.050 0.154 604 Planarity : 0.006 0.043 684 Dihedral : 7.607 50.210 632 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.85 % Allowed : 3.81 % Favored : 95.34 % Rotamer: Outliers : 0.81 % Allowed : 11.83 % Favored : 87.37 % 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 (0.36), residues: 512 helix: None (None), residues: 0 sheet: 0.47 (0.25), residues: 312 loop : 0.16 (0.51), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.004 TRP B 92 HIS 0.006 0.003 HIS C 87 PHE 0.016 0.004 PHE B 29 TYR 0.014 0.004 TYR D 22 ARG 0.007 0.001 ARG A 103 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 68 time to evaluate : 0.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 ARG cc_start: 0.8137 (ttm-80) cc_final: 0.7567 (ttm110) REVERT: B 103 ARG cc_start: 0.8173 (ttm-80) cc_final: 0.7488 (ttp80) REVERT: C 103 ARG cc_start: 0.8138 (ttm-80) cc_final: 0.7603 (ttm110) outliers start: 3 outliers final: 1 residues processed: 68 average time/residue: 1.5562 time to fit residues: 108.5614 Evaluate side-chains 68 residues out of total 332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 67 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 107 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 26 optimal weight: 9.9990 chunk 39 optimal weight: 20.0000 chunk 25 optimal weight: 10.0000 chunk 46 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 21 optimal weight: 7.9990 chunk 18 optimal weight: 7.9990 chunk 27 optimal weight: 8.9990 chunk 13 optimal weight: 5.9990 chunk 9 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- 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: 0.8087 moved from start: 0.3030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 3944 Z= 0.254 Angle : 0.675 4.924 5400 Z= 0.377 Chirality : 0.044 0.148 604 Planarity : 0.004 0.023 684 Dihedral : 7.138 46.680 632 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.64 % Allowed : 3.60 % Favored : 95.76 % Rotamer: Outliers : 0.27 % Allowed : 12.63 % Favored : 87.10 % 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: 0.64 (0.37), residues: 512 helix: None (None), residues: 0 sheet: 0.60 (0.26), residues: 304 loop : 0.34 (0.50), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP D 92 HIS 0.004 0.002 HIS C 87 PHE 0.017 0.004 PHE B 29 TYR 0.013 0.002 TYR D 22 ARG 0.003 0.001 ARG A 103 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 75 time to evaluate : 0.363 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 ARG cc_start: 0.8069 (ttm-80) cc_final: 0.7515 (ttm110) REVERT: B 103 ARG cc_start: 0.8169 (ttm-80) cc_final: 0.7456 (ttp80) REVERT: C 27 SER cc_start: 0.8195 (m) cc_final: 0.7943 (m) REVERT: C 103 ARG cc_start: 0.8078 (ttm-80) cc_final: 0.7531 (ttm110) REVERT: D 103 ARG cc_start: 0.8184 (ttm-80) cc_final: 0.7547 (ttm110) outliers start: 1 outliers final: 1 residues processed: 75 average time/residue: 1.4037 time to fit residues: 108.2089 Evaluate side-chains 72 residues out of total 332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 71 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 107 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 29 optimal weight: 6.9990 chunk 31 optimal weight: 20.0000 chunk 22 optimal weight: 9.9990 chunk 4 optimal weight: 5.9990 chunk 36 optimal weight: 20.0000 chunk 42 optimal weight: 9.9990 chunk 44 optimal weight: 6.9990 chunk 40 optimal weight: 2.9990 chunk 43 optimal weight: 6.9990 chunk 25 optimal weight: 8.9990 chunk 18 optimal weight: 1.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- 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: 0.8094 moved from start: 0.3070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 3944 Z= 0.326 Angle : 0.752 6.049 5400 Z= 0.414 Chirality : 0.048 0.197 604 Planarity : 0.005 0.030 684 Dihedral : 7.373 48.657 632 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.85 % Allowed : 4.03 % Favored : 95.13 % Rotamer: Outliers : 0.27 % Allowed : 12.37 % Favored : 87.37 % 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: 0.49 (0.37), residues: 512 helix: None (None), residues: 0 sheet: 0.55 (0.26), residues: 304 loop : 0.15 (0.49), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP B 92 HIS 0.005 0.002 HIS C 87 PHE 0.014 0.003 PHE C 29 TYR 0.015 0.003 TYR A 22 ARG 0.005 0.001 ARG A 103 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 72 time to evaluate : 0.659 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 ARG cc_start: 0.8109 (ttm-80) cc_final: 0.7585 (ttm110) REVERT: B 103 ARG cc_start: 0.8174 (ttm-80) cc_final: 0.7460 (ttp80) REVERT: C 103 ARG cc_start: 0.8124 (ttm-80) cc_final: 0.7602 (ttm110) outliers start: 1 outliers final: 1 residues processed: 72 average time/residue: 1.5892 time to fit residues: 117.7762 Evaluate side-chains 72 residues out of total 332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 71 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 107 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 33 optimal weight: 20.0000 chunk 13 optimal weight: 0.8980 chunk 38 optimal weight: 10.0000 chunk 40 optimal weight: 0.7980 chunk 42 optimal weight: 3.9990 chunk 28 optimal weight: 8.9990 chunk 45 optimal weight: 0.9980 chunk 27 optimal weight: 5.9990 chunk 21 optimal weight: 9.9990 chunk 31 optimal weight: 5.9990 chunk 47 optimal weight: 0.7980 overall best weight: 1.4982 ------------------------------------------------------------------------------- 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: 0.8059 moved from start: 0.3089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 3944 Z= 0.159 Angle : 0.604 7.179 5400 Z= 0.326 Chirality : 0.042 0.153 604 Planarity : 0.003 0.014 684 Dihedral : 6.707 43.559 632 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 0.00 % Allowed : 13.17 % Favored : 86.83 % 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: 0.90 (0.36), residues: 512 helix: None (None), residues: 0 sheet: 0.83 (0.26), residues: 296 loop : 0.42 (0.47), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 92 HIS 0.002 0.001 HIS C 87 PHE 0.006 0.002 PHE C 29 TYR 0.009 0.001 TYR C 22 ARG 0.002 0.000 ARG A 103 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 72 time to evaluate : 0.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 ARG cc_start: 0.8038 (ttm-80) cc_final: 0.7490 (ttm110) REVERT: B 103 ARG cc_start: 0.8152 (ttm-80) cc_final: 0.7437 (ttp80) REVERT: C 103 ARG cc_start: 0.8063 (ttm-80) cc_final: 0.7511 (ttm110) REVERT: D 103 ARG cc_start: 0.8193 (ttm-80) cc_final: 0.7532 (ttm110) outliers start: 0 outliers final: 0 residues processed: 72 average time/residue: 1.4350 time to fit residues: 106.2321 Evaluate side-chains 72 residues out of total 332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 72 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 44 optimal weight: 3.9990 chunk 38 optimal weight: 20.0000 chunk 3 optimal weight: 4.9990 chunk 29 optimal weight: 9.9990 chunk 23 optimal weight: 8.9990 chunk 30 optimal weight: 4.9990 chunk 40 optimal weight: 0.0170 chunk 11 optimal weight: 9.9990 chunk 35 optimal weight: 5.9990 chunk 5 optimal weight: 0.0000 chunk 10 optimal weight: 0.9980 overall best weight: 2.0026 ------------------------------------------------------------------------------- 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: 0.8063 moved from start: 0.3153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3944 Z= 0.183 Angle : 0.629 7.166 5400 Z= 0.340 Chirality : 0.043 0.159 604 Planarity : 0.003 0.016 684 Dihedral : 6.787 45.043 632 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 0.00 % Allowed : 12.63 % Favored : 87.37 % 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: 0.91 (0.36), residues: 512 helix: None (None), residues: 0 sheet: 0.81 (0.26), residues: 296 loop : 0.47 (0.47), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 92 HIS 0.003 0.001 HIS C 87 PHE 0.006 0.002 PHE A 29 TYR 0.007 0.001 TYR A 96 ARG 0.002 0.000 ARG A 103 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 71 time to evaluate : 0.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 ARG cc_start: 0.8039 (ttm-80) cc_final: 0.7489 (ttm110) REVERT: B 103 ARG cc_start: 0.8154 (ttm-80) cc_final: 0.7439 (ttp80) REVERT: C 103 ARG cc_start: 0.8081 (ttm-80) cc_final: 0.7442 (ttm110) REVERT: D 103 ARG cc_start: 0.8186 (ttm-80) cc_final: 0.7536 (ttm110) outliers start: 0 outliers final: 0 residues processed: 71 average time/residue: 1.5430 time to fit residues: 112.4372 Evaluate side-chains 71 residues out of total 332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 71 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 38 optimal weight: 20.0000 chunk 15 optimal weight: 0.3980 chunk 39 optimal weight: 10.0000 chunk 4 optimal weight: 10.0000 chunk 7 optimal weight: 9.9990 chunk 33 optimal weight: 20.0000 chunk 2 optimal weight: 3.9990 chunk 27 optimal weight: 0.0010 chunk 43 optimal weight: 20.0000 chunk 25 optimal weight: 10.0000 chunk 32 optimal weight: 4.9990 overall best weight: 3.8792 ------------------------------------------------------------------------------- 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 = 0.4095 r_free = 0.4095 target = 0.173175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.150456 restraints weight = 3561.300| |-----------------------------------------------------------------------------| r_work (start): 0.3829 rms_B_bonded: 1.05 r_work: 0.3738 rms_B_bonded: 1.41 restraints_weight: 0.5000 r_work: 0.3630 rms_B_bonded: 2.37 restraints_weight: 0.2500 r_work (final): 0.3630 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3631 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3631 r_free = 0.3631 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3625 r_free = 0.3625 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3625 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.3155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3944 Z= 0.277 Angle : 0.700 6.327 5400 Z= 0.384 Chirality : 0.047 0.197 604 Planarity : 0.004 0.024 684 Dihedral : 7.154 47.868 632 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 0.00 % Allowed : 12.63 % Favored : 87.37 % 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: 0.85 (0.37), residues: 512 helix: None (None), residues: 0 sheet: 0.75 (0.27), residues: 296 loop : 0.45 (0.49), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP D 92 HIS 0.005 0.002 HIS C 87 PHE 0.010 0.003 PHE A 29 TYR 0.016 0.002 TYR A 22 ARG 0.004 0.001 ARG A 103 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2267.75 seconds wall clock time: 44 minutes 28.83 seconds (2668.83 seconds total)