Starting phenix.real_space_refine on Sat Dec 9 08:42:27 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l1u_0803/12_2023/6l1u_0803_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l1u_0803/12_2023/6l1u_0803.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.37 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l1u_0803/12_2023/6l1u_0803.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l1u_0803/12_2023/6l1u_0803.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l1u_0803/12_2023/6l1u_0803_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l1u_0803/12_2023/6l1u_0803_updated.pdb" } resolution = 3.37 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= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 15 5.49 5 S 15 5.16 5 C 6540 2.51 5 N 1815 2.21 5 O 2130 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 35": "OE1" <-> "OE2" Residue "A GLU 57": "OE1" <-> "OE2" Residue "B GLU 35": "OE1" <-> "OE2" Residue "B GLU 57": "OE1" <-> "OE2" Residue "C GLU 35": "OE1" <-> "OE2" Residue "C GLU 57": "OE1" <-> "OE2" Residue "D GLU 35": "OE1" <-> "OE2" Residue "D GLU 57": "OE1" <-> "OE2" Residue "E GLU 35": "OE1" <-> "OE2" Residue "E GLU 57": "OE1" <-> "OE2" Residue "F GLU 35": "OE1" <-> "OE2" Residue "F GLU 57": "OE1" <-> "OE2" Residue "G GLU 35": "OE1" <-> "OE2" Residue "G GLU 57": "OE1" <-> "OE2" Residue "H GLU 35": "OE1" <-> "OE2" Residue "H GLU 57": "OE1" <-> "OE2" Residue "I GLU 35": "OE1" <-> "OE2" Residue "I GLU 57": "OE1" <-> "OE2" Residue "J GLU 35": "OE1" <-> "OE2" Residue "J GLU 57": "OE1" <-> "OE2" Residue "K GLU 35": "OE1" <-> "OE2" Residue "K GLU 57": "OE1" <-> "OE2" Residue "L GLU 35": "OE1" <-> "OE2" Residue "L GLU 57": "OE1" <-> "OE2" Residue "M GLU 35": "OE1" <-> "OE2" Residue "M GLU 57": "OE1" <-> "OE2" Residue "N GLU 35": "OE1" <-> "OE2" Residue "N GLU 57": "OE1" <-> "OE2" Residue "O GLU 35": "OE1" <-> "OE2" Residue "O GLU 57": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 10515 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 701 Classifications: {'peptide': 100} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 99} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'PTR:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 701 Classifications: {'peptide': 100} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 99} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'PTR:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 701 Classifications: {'peptide': 100} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 99} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'PTR:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 701 Classifications: {'peptide': 100} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 99} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'PTR:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 701 Classifications: {'peptide': 100} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 99} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'PTR:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "F" Number of atoms: 701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 701 Classifications: {'peptide': 100} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 99} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'PTR:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "G" Number of atoms: 701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 701 Classifications: {'peptide': 100} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 99} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'PTR:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "H" Number of atoms: 701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 701 Classifications: {'peptide': 100} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 99} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'PTR:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "I" Number of atoms: 701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 701 Classifications: {'peptide': 100} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 99} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'PTR:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "J" Number of atoms: 701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 701 Classifications: {'peptide': 100} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 99} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'PTR:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "K" Number of atoms: 701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 701 Classifications: {'peptide': 100} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 99} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'PTR:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "L" Number of atoms: 701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 701 Classifications: {'peptide': 100} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 99} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'PTR:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "M" Number of atoms: 701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 701 Classifications: {'peptide': 100} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 99} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'PTR:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "N" Number of atoms: 701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 701 Classifications: {'peptide': 100} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 99} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'PTR:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "O" Number of atoms: 701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 701 Classifications: {'peptide': 100} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 99} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'PTR:plan-2': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 5.62, per 1000 atoms: 0.53 Number of scatterers: 10515 At special positions: 0 Unit cell: (197.357, 159.454, 56.201, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 15 16.00 P 15 15.00 O 2130 8.00 N 1815 7.00 C 6540 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.25 Conformation dependent library (CDL) restraints added in 2.1 seconds 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2580 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 0 helices and 0 sheets defined 0.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.55 Creating SS restraints... No hydrogen bonds 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: 0.01 Time building geometry restraints manager: 4.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 3465 1.33 - 1.45: 810 1.45 - 1.57: 6240 1.57 - 1.68: 15 1.68 - 1.80: 30 Bond restraints: 10560 Sorted by residual: bond pdb=" OH PTR G 39 " pdb=" P PTR G 39 " ideal model delta sigma weight residual 1.769 1.602 0.167 2.00e-02 2.50e+03 6.96e+01 bond pdb=" OH PTR N 39 " pdb=" P PTR N 39 " ideal model delta sigma weight residual 1.769 1.602 0.167 2.00e-02 2.50e+03 6.96e+01 bond pdb=" OH PTR D 39 " pdb=" P PTR D 39 " ideal model delta sigma weight residual 1.769 1.602 0.167 2.00e-02 2.50e+03 6.94e+01 bond pdb=" OH PTR M 39 " pdb=" P PTR M 39 " ideal model delta sigma weight residual 1.769 1.602 0.167 2.00e-02 2.50e+03 6.94e+01 bond pdb=" OH PTR C 39 " pdb=" P PTR C 39 " ideal model delta sigma weight residual 1.769 1.602 0.167 2.00e-02 2.50e+03 6.93e+01 ... (remaining 10555 not shown) Histogram of bond angle deviations from ideal: 100.35 - 106.52: 105 106.52 - 112.68: 6266 112.68 - 118.85: 2675 118.85 - 125.01: 5144 125.01 - 131.18: 15 Bond angle restraints: 14205 Sorted by residual: angle pdb=" OH PTR K 39 " pdb=" P PTR K 39 " pdb=" O2P PTR K 39 " ideal model delta sigma weight residual 99.92 109.42 -9.50 3.00e+00 1.11e-01 1.00e+01 angle pdb=" OH PTR M 39 " pdb=" P PTR M 39 " pdb=" O2P PTR M 39 " ideal model delta sigma weight residual 99.92 109.40 -9.48 3.00e+00 1.11e-01 9.98e+00 angle pdb=" OH PTR J 39 " pdb=" P PTR J 39 " pdb=" O2P PTR J 39 " ideal model delta sigma weight residual 99.92 109.40 -9.48 3.00e+00 1.11e-01 9.98e+00 angle pdb=" OH PTR L 39 " pdb=" P PTR L 39 " pdb=" O2P PTR L 39 " ideal model delta sigma weight residual 99.92 109.39 -9.47 3.00e+00 1.11e-01 9.96e+00 angle pdb=" OH PTR C 39 " pdb=" P PTR C 39 " pdb=" O2P PTR C 39 " ideal model delta sigma weight residual 99.92 109.39 -9.47 3.00e+00 1.11e-01 9.96e+00 ... (remaining 14200 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.25: 5715 17.25 - 34.50: 405 34.50 - 51.75: 120 51.75 - 69.00: 15 69.00 - 86.25: 30 Dihedral angle restraints: 6285 sinusoidal: 2220 harmonic: 4065 Sorted by residual: dihedral pdb=" CA ALA G 29 " pdb=" C ALA G 29 " pdb=" N ALA G 30 " pdb=" CA ALA G 30 " ideal model delta harmonic sigma weight residual 180.00 161.32 18.68 0 5.00e+00 4.00e-02 1.40e+01 dihedral pdb=" CA ALA J 29 " pdb=" C ALA J 29 " pdb=" N ALA J 30 " pdb=" CA ALA J 30 " ideal model delta harmonic sigma weight residual 180.00 161.36 18.64 0 5.00e+00 4.00e-02 1.39e+01 dihedral pdb=" CA ALA E 29 " pdb=" C ALA E 29 " pdb=" N ALA E 30 " pdb=" CA ALA E 30 " ideal model delta harmonic sigma weight residual 180.00 161.37 18.63 0 5.00e+00 4.00e-02 1.39e+01 ... (remaining 6282 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1210 0.056 - 0.113: 456 0.113 - 0.169: 89 0.169 - 0.225: 0 0.225 - 0.281: 15 Chirality restraints: 1770 Sorted by residual: chirality pdb=" CB VAL F 77 " pdb=" CA VAL F 77 " pdb=" CG1 VAL F 77 " pdb=" CG2 VAL F 77 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 1.98e+00 chirality pdb=" CB VAL L 77 " pdb=" CA VAL L 77 " pdb=" CG1 VAL L 77 " pdb=" CG2 VAL L 77 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 1.97e+00 chirality pdb=" CB VAL N 77 " pdb=" CA VAL N 77 " pdb=" CG1 VAL N 77 " pdb=" CG2 VAL N 77 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 1.96e+00 ... (remaining 1767 not shown) Planarity restraints: 1770 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU D 13 " -0.005 2.00e-02 2.50e+03 1.02e-02 1.04e+00 pdb=" CD GLU D 13 " 0.018 2.00e-02 2.50e+03 pdb=" OE1 GLU D 13 " -0.006 2.00e-02 2.50e+03 pdb=" OE2 GLU D 13 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU L 13 " -0.005 2.00e-02 2.50e+03 1.02e-02 1.04e+00 pdb=" CD GLU L 13 " 0.018 2.00e-02 2.50e+03 pdb=" OE1 GLU L 13 " -0.006 2.00e-02 2.50e+03 pdb=" OE2 GLU L 13 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU M 13 " -0.005 2.00e-02 2.50e+03 1.01e-02 1.03e+00 pdb=" CD GLU M 13 " 0.018 2.00e-02 2.50e+03 pdb=" OE1 GLU M 13 " -0.006 2.00e-02 2.50e+03 pdb=" OE2 GLU M 13 " -0.006 2.00e-02 2.50e+03 ... (remaining 1767 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 414 2.69 - 3.24: 10255 3.24 - 3.79: 15559 3.79 - 4.35: 18959 4.35 - 4.90: 37441 Nonbonded interactions: 82628 Sorted by model distance: nonbonded pdb=" O SER D 9 " pdb=" OG SER D 9 " model vdw 2.138 2.440 nonbonded pdb=" O SER A 9 " pdb=" OG SER A 9 " model vdw 2.138 2.440 nonbonded pdb=" O SER N 9 " pdb=" OG SER N 9 " model vdw 2.138 2.440 nonbonded pdb=" O SER J 9 " pdb=" OG SER J 9 " model vdw 2.138 2.440 nonbonded pdb=" O SER G 9 " pdb=" OG SER G 9 " model vdw 2.138 2.440 ... (remaining 82623 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' } 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: 2.100 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: 7.140 Check model and map are aligned: 0.170 Set scattering table: 0.110 Process input model: 28.020 Find NCS groups from input model: 0.710 Set up NCS constraints: 0.090 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:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 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 : 0.011 0.167 10560 Z= 0.515 Angle : 0.901 9.499 14205 Z= 0.449 Chirality : 0.063 0.281 1770 Planarity : 0.002 0.010 1770 Dihedral : 15.318 86.255 3705 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 15.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.79 % Favored : 84.21 % Rotamer: Outliers : 0.00 % Allowed : 17.65 % Favored : 82.35 % 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: -6.06 (0.10), residues: 1425 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.61 (0.08), residues: 1425 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS H 50 PHE 0.015 0.003 PHE F 94 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 326 time to evaluate : 1.834 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 326 average time/residue: 0.2148 time to fit residues: 99.3948 Evaluate side-chains 249 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 249 time to evaluate : 1.265 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 126 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 38 optimal weight: 10.0000 chunk 76 optimal weight: 5.9990 chunk 60 optimal weight: 9.9990 chunk 117 optimal weight: 4.9990 chunk 45 optimal weight: 8.9990 chunk 71 optimal weight: 9.9990 chunk 87 optimal weight: 0.0980 chunk 136 optimal weight: 3.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 GLN B 62 GLN B 99 GLN C 62 GLN C 99 GLN D 62 GLN D 99 GLN E 62 GLN E 99 GLN F 62 GLN F 99 GLN G 62 GLN H 62 GLN I 62 GLN J 62 GLN K 62 GLN ** K 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 62 GLN M 62 GLN N 62 GLN O 62 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.2433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10560 Z= 0.147 Angle : 0.557 8.023 14205 Z= 0.304 Chirality : 0.049 0.138 1770 Planarity : 0.002 0.014 1770 Dihedral : 5.992 24.785 1515 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.12 % Favored : 86.88 % Rotamer: Outliers : 5.00 % Allowed : 20.88 % Favored : 74.12 % 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: -5.71 (0.11), residues: 1425 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.34 (0.09), residues: 1425 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS K 50 PHE 0.016 0.003 PHE C 94 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 299 time to evaluate : 1.204 Fit side-chains revert: symmetry clash outliers start: 51 outliers final: 40 residues processed: 326 average time/residue: 0.1751 time to fit residues: 85.1239 Evaluate side-chains 308 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 268 time to evaluate : 1.193 Switching outliers to nearest non-outliers outliers start: 40 outliers final: 0 residues processed: 40 average time/residue: 0.0957 time to fit residues: 8.5823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 75 optimal weight: 9.9990 chunk 42 optimal weight: 5.9990 chunk 113 optimal weight: 10.0000 chunk 92 optimal weight: 2.9990 chunk 37 optimal weight: 0.5980 chunk 136 optimal weight: 10.0000 chunk 147 optimal weight: 2.9990 chunk 121 optimal weight: 20.0000 chunk 135 optimal weight: 10.0000 chunk 46 optimal weight: 0.0470 chunk 109 optimal weight: 9.9990 overall best weight: 2.5284 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 99 GLN C 99 GLN D 99 GLN F 99 GLN K 99 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.3102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10560 Z= 0.187 Angle : 0.575 6.874 14205 Z= 0.313 Chirality : 0.050 0.137 1770 Planarity : 0.002 0.014 1770 Dihedral : 6.040 27.329 1515 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.58 % Favored : 84.42 % Rotamer: Outliers : 5.20 % Allowed : 22.55 % Favored : 72.25 % 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: -5.47 (0.12), residues: 1425 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.16 (0.09), residues: 1425 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS O 50 PHE 0.017 0.003 PHE C 94 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 281 time to evaluate : 1.289 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 53 outliers final: 31 residues processed: 316 average time/residue: 0.1791 time to fit residues: 85.0049 Evaluate side-chains 302 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 271 time to evaluate : 1.207 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 0 residues processed: 31 average time/residue: 0.1012 time to fit residues: 7.3767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 134 optimal weight: 9.9990 chunk 102 optimal weight: 0.0020 chunk 70 optimal weight: 9.9990 chunk 15 optimal weight: 10.0000 chunk 65 optimal weight: 9.9990 chunk 91 optimal weight: 0.0470 chunk 136 optimal weight: 9.9990 chunk 144 optimal weight: 3.9990 chunk 71 optimal weight: 6.9990 chunk 129 optimal weight: 1.9990 chunk 39 optimal weight: 10.0000 overall best weight: 2.6092 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 99 GLN C 99 GLN F 99 GLN M 24 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.3417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 10560 Z= 0.187 Angle : 0.565 8.043 14205 Z= 0.307 Chirality : 0.049 0.139 1770 Planarity : 0.002 0.012 1770 Dihedral : 5.993 27.980 1515 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.04 % Favored : 85.96 % Rotamer: Outliers : 4.80 % Allowed : 21.67 % Favored : 73.53 % 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: -5.33 (0.13), residues: 1425 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.06 (0.10), residues: 1425 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS O 50 PHE 0.017 0.003 PHE C 94 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 288 time to evaluate : 1.190 Fit side-chains outliers start: 49 outliers final: 40 residues processed: 313 average time/residue: 0.1757 time to fit residues: 82.4544 Evaluate side-chains 316 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 276 time to evaluate : 1.234 Switching outliers to nearest non-outliers outliers start: 40 outliers final: 0 residues processed: 40 average time/residue: 0.0999 time to fit residues: 8.8838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 120 optimal weight: 20.0000 chunk 82 optimal weight: 0.9990 chunk 2 optimal weight: 6.9990 chunk 107 optimal weight: 0.8980 chunk 59 optimal weight: 10.0000 chunk 123 optimal weight: 6.9990 chunk 100 optimal weight: 10.0000 chunk 0 optimal weight: 8.9990 chunk 74 optimal weight: 5.9990 chunk 130 optimal weight: 4.9990 chunk 36 optimal weight: 9.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 99 GLN C 99 GLN F 99 GLN M 24 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.3624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 10560 Z= 0.273 Angle : 0.647 7.308 14205 Z= 0.348 Chirality : 0.051 0.143 1770 Planarity : 0.002 0.011 1770 Dihedral : 6.353 29.220 1515 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.84 % Favored : 83.16 % Rotamer: Outliers : 4.61 % Allowed : 22.75 % Favored : 72.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.26 (0.13), residues: 1425 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.00 (0.10), residues: 1425 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS O 50 PHE 0.020 0.003 PHE C 94 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 285 time to evaluate : 1.246 Fit side-chains outliers start: 47 outliers final: 37 residues processed: 315 average time/residue: 0.1884 time to fit residues: 88.9586 Evaluate side-chains 314 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 277 time to evaluate : 1.201 Switching outliers to nearest non-outliers outliers start: 37 outliers final: 0 residues processed: 37 average time/residue: 0.1038 time to fit residues: 8.5626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 48 optimal weight: 0.0570 chunk 130 optimal weight: 9.9990 chunk 28 optimal weight: 9.9990 chunk 85 optimal weight: 10.0000 chunk 35 optimal weight: 7.9990 chunk 145 optimal weight: 0.9980 chunk 120 optimal weight: 5.9990 chunk 67 optimal weight: 3.9990 chunk 12 optimal weight: 0.5980 chunk 76 optimal weight: 1.9990 chunk 139 optimal weight: 10.0000 overall best weight: 1.5302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 99 GLN C 99 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.3797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10560 Z= 0.123 Angle : 0.519 6.855 14205 Z= 0.285 Chirality : 0.049 0.136 1770 Planarity : 0.002 0.009 1770 Dihedral : 5.831 31.990 1515 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.00 % Favored : 88.00 % Rotamer: Outliers : 2.25 % Allowed : 24.12 % Favored : 73.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.12 (0.13), residues: 1425 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.89 (0.10), residues: 1425 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS H 50 PHE 0.019 0.002 PHE K 4 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 299 time to evaluate : 1.213 Fit side-chains outliers start: 23 outliers final: 14 residues processed: 314 average time/residue: 0.1808 time to fit residues: 85.4764 Evaluate side-chains 292 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 278 time to evaluate : 1.224 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1091 time to fit residues: 4.3632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 16 optimal weight: 10.0000 chunk 82 optimal weight: 5.9990 chunk 105 optimal weight: 2.9990 chunk 122 optimal weight: 10.0000 chunk 81 optimal weight: 10.0000 chunk 144 optimal weight: 8.9990 chunk 90 optimal weight: 6.9990 chunk 88 optimal weight: 6.9990 chunk 66 optimal weight: 8.9990 chunk 89 optimal weight: 6.9990 chunk 57 optimal weight: 0.5980 overall best weight: 4.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 99 GLN C 99 GLN F 99 GLN M 24 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.3831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.043 10560 Z= 0.318 Angle : 0.689 8.105 14205 Z= 0.368 Chirality : 0.053 0.168 1770 Planarity : 0.002 0.010 1770 Dihedral : 6.440 32.200 1515 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 12.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.61 % Favored : 82.39 % Rotamer: Outliers : 3.53 % Allowed : 24.31 % Favored : 72.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.13 (0.13), residues: 1425 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.90 (0.10), residues: 1425 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS O 50 PHE 0.021 0.003 PHE I 94 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 281 time to evaluate : 1.257 Fit side-chains outliers start: 36 outliers final: 28 residues processed: 298 average time/residue: 0.1789 time to fit residues: 80.3551 Evaluate side-chains 299 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 271 time to evaluate : 1.164 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 0 residues processed: 28 average time/residue: 0.0977 time to fit residues: 6.5516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 86 optimal weight: 2.9990 chunk 43 optimal weight: 6.9990 chunk 28 optimal weight: 6.9990 chunk 91 optimal weight: 5.9990 chunk 98 optimal weight: 0.9980 chunk 71 optimal weight: 3.9990 chunk 13 optimal weight: 5.9990 chunk 113 optimal weight: 5.9990 chunk 131 optimal weight: 9.9990 chunk 138 optimal weight: 9.9990 chunk 126 optimal weight: 7.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 99 GLN C 99 GLN F 99 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.3927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 10560 Z= 0.272 Angle : 0.666 7.752 14205 Z= 0.355 Chirality : 0.052 0.145 1770 Planarity : 0.002 0.010 1770 Dihedral : 6.458 35.707 1515 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.74 % Favored : 85.26 % Rotamer: Outliers : 2.84 % Allowed : 24.31 % Favored : 72.84 % 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: -5.11 (0.14), residues: 1425 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.89 (0.10), residues: 1425 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS O 50 PHE 0.019 0.003 PHE I 94 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 278 time to evaluate : 1.216 Fit side-chains outliers start: 29 outliers final: 24 residues processed: 295 average time/residue: 0.1807 time to fit residues: 79.7899 Evaluate side-chains 299 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 275 time to evaluate : 1.267 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 0.1073 time to fit residues: 6.2709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 134 optimal weight: 9.9990 chunk 138 optimal weight: 10.0000 chunk 81 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 105 optimal weight: 3.9990 chunk 41 optimal weight: 4.9990 chunk 121 optimal weight: 2.9990 chunk 127 optimal weight: 6.9990 chunk 88 optimal weight: 4.9990 chunk 142 optimal weight: 9.9990 chunk 86 optimal weight: 4.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 99 GLN C 99 GLN F 99 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.3972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 10560 Z= 0.225 Angle : 0.634 9.569 14205 Z= 0.338 Chirality : 0.051 0.144 1770 Planarity : 0.002 0.010 1770 Dihedral : 6.340 38.450 1515 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.72 % Favored : 84.28 % Rotamer: Outliers : 1.47 % Allowed : 24.22 % Favored : 74.31 % 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: -5.05 (0.14), residues: 1425 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.84 (0.10), residues: 1425 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS O 50 PHE 0.018 0.003 PHE I 94 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 284 time to evaluate : 1.234 Fit side-chains outliers start: 15 outliers final: 11 residues processed: 291 average time/residue: 0.1822 time to fit residues: 78.9390 Evaluate side-chains 283 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 272 time to evaluate : 1.185 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1162 time to fit residues: 3.8272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 67 optimal weight: 1.9990 chunk 99 optimal weight: 0.6980 chunk 149 optimal weight: 2.9990 chunk 137 optimal weight: 0.8980 chunk 118 optimal weight: 9.9990 chunk 12 optimal weight: 6.9990 chunk 91 optimal weight: 7.9990 chunk 72 optimal weight: 0.9980 chunk 94 optimal weight: 5.9990 chunk 126 optimal weight: 9.9990 chunk 36 optimal weight: 3.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 99 GLN C 99 GLN E 99 GLN F 99 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.4122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10560 Z= 0.128 Angle : 0.551 8.426 14205 Z= 0.297 Chirality : 0.049 0.138 1770 Planarity : 0.002 0.009 1770 Dihedral : 5.906 41.483 1515 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.49 % Favored : 87.51 % Rotamer: Outliers : 0.49 % Allowed : 25.29 % Favored : 74.22 % 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: -4.92 (0.14), residues: 1425 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.75 (0.11), residues: 1425 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS K 50 PHE 0.021 0.003 PHE N 4 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 291 time to evaluate : 1.223 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 293 average time/residue: 0.1808 time to fit residues: 79.5317 Evaluate side-chains 277 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 274 time to evaluate : 1.205 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1115 time to fit residues: 2.1831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 109 optimal weight: 9.9990 chunk 17 optimal weight: 2.9990 chunk 33 optimal weight: 6.9990 chunk 119 optimal weight: 10.0000 chunk 49 optimal weight: 6.9990 chunk 122 optimal weight: 7.9990 chunk 15 optimal weight: 10.0000 chunk 21 optimal weight: 8.9990 chunk 104 optimal weight: 3.9990 chunk 6 optimal weight: 0.5980 chunk 86 optimal weight: 10.0000 overall best weight: 4.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 99 GLN C 99 GLN E 99 GLN F 99 GLN M 24 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.116057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.099621 restraints weight = 19004.052| |-----------------------------------------------------------------------------| r_work (start): 0.3658 rms_B_bonded: 2.74 r_work: 0.3545 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work (final): 0.3545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.4053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.044 10560 Z= 0.296 Angle : 0.694 8.174 14205 Z= 0.368 Chirality : 0.053 0.159 1770 Planarity : 0.002 0.009 1770 Dihedral : 6.480 37.389 1515 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.98 % Favored : 83.02 % Rotamer: Outliers : 1.37 % Allowed : 26.18 % Favored : 72.45 % 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: -4.98 (0.14), residues: 1425 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.79 (0.11), residues: 1425 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS O 50 PHE 0.020 0.003 PHE I 94 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2563.26 seconds wall clock time: 47 minutes 28.64 seconds (2848.64 seconds total)