Starting phenix.real_space_refine on Thu Dec 7 17:03:36 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u1k_41815/12_2023/8u1k_41815.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u1k_41815/12_2023/8u1k_41815.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u1k_41815/12_2023/8u1k_41815.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u1k_41815/12_2023/8u1k_41815.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u1k_41815/12_2023/8u1k_41815.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u1k_41815/12_2023/8u1k_41815.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.017 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: 3 Type Number sf(0) Gaussians C 1970 2.51 5 N 500 2.21 5 O 590 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 3060 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 306 Classifications: {'peptide': 45} Link IDs: {'TRANS': 44} Chain: "B" Number of atoms: 306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 306 Classifications: {'peptide': 45} Link IDs: {'TRANS': 44} Chain: "C" Number of atoms: 306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 306 Classifications: {'peptide': 45} Link IDs: {'TRANS': 44} Chain: "D" Number of atoms: 306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 306 Classifications: {'peptide': 45} Link IDs: {'TRANS': 44} Chain: "E" Number of atoms: 306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 306 Classifications: {'peptide': 45} Link IDs: {'TRANS': 44} Chain: "F" Number of atoms: 306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 306 Classifications: {'peptide': 45} Link IDs: {'TRANS': 44} Chain: "G" Number of atoms: 306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 306 Classifications: {'peptide': 45} Link IDs: {'TRANS': 44} Chain: "H" Number of atoms: 306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 306 Classifications: {'peptide': 45} Link IDs: {'TRANS': 44} Chain: "I" Number of atoms: 306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 306 Classifications: {'peptide': 45} Link IDs: {'TRANS': 44} Chain: "J" Number of atoms: 306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 306 Classifications: {'peptide': 45} Link IDs: {'TRANS': 44} Time building chain proxies: 2.11, per 1000 atoms: 0.69 Number of scatterers: 3060 At special positions: 0 Unit cell: (58.38, 57.546, 118.428, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 590 8.00 N 500 7.00 C 1970 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: 1.35 Conformation dependent library (CDL) restraints added in 645.9 milliseconds 860 Ramachandran restraints generated. 430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 820 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 0 sheets defined 77.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'A' and resid 3 through 5 No H-bonds generated for 'chain 'A' and resid 3 through 5' Processing helix chain 'A' and resid 6 through 11 Processing helix chain 'A' and resid 17 through 42 removed outlier: 4.377A pdb=" N THR A 23 " --> pdb=" O THR A 19 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N THR A 30 " --> pdb=" O THR A 26 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N THR A 41 " --> pdb=" O ALA A 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 5 No H-bonds generated for 'chain 'B' and resid 3 through 5' Processing helix chain 'B' and resid 6 through 11 Processing helix chain 'B' and resid 17 through 42 removed outlier: 4.377A pdb=" N THR B 23 " --> pdb=" O THR B 19 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N THR B 30 " --> pdb=" O THR B 26 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N THR B 41 " --> pdb=" O ALA B 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 5 No H-bonds generated for 'chain 'C' and resid 3 through 5' Processing helix chain 'C' and resid 6 through 11 Processing helix chain 'C' and resid 17 through 42 removed outlier: 4.378A pdb=" N THR C 23 " --> pdb=" O THR C 19 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N THR C 30 " --> pdb=" O THR C 26 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N THR C 41 " --> pdb=" O ALA C 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 3 through 5 No H-bonds generated for 'chain 'D' and resid 3 through 5' Processing helix chain 'D' and resid 6 through 11 Processing helix chain 'D' and resid 17 through 42 removed outlier: 4.377A pdb=" N THR D 23 " --> pdb=" O THR D 19 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N THR D 30 " --> pdb=" O THR D 26 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N THR D 41 " --> pdb=" O ALA D 37 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 5 No H-bonds generated for 'chain 'E' and resid 3 through 5' Processing helix chain 'E' and resid 6 through 11 Processing helix chain 'E' and resid 17 through 42 removed outlier: 4.378A pdb=" N THR E 23 " --> pdb=" O THR E 19 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N THR E 30 " --> pdb=" O THR E 26 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N THR E 41 " --> pdb=" O ALA E 37 " (cutoff:3.500A) Processing helix chain 'F' and resid 3 through 5 No H-bonds generated for 'chain 'F' and resid 3 through 5' Processing helix chain 'F' and resid 6 through 11 Processing helix chain 'F' and resid 17 through 42 removed outlier: 4.377A pdb=" N THR F 23 " --> pdb=" O THR F 19 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N THR F 30 " --> pdb=" O THR F 26 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N THR F 41 " --> pdb=" O ALA F 37 " (cutoff:3.500A) Processing helix chain 'G' and resid 3 through 5 No H-bonds generated for 'chain 'G' and resid 3 through 5' Processing helix chain 'G' and resid 6 through 11 Processing helix chain 'G' and resid 17 through 42 removed outlier: 4.378A pdb=" N THR G 23 " --> pdb=" O THR G 19 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N THR G 30 " --> pdb=" O THR G 26 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N THR G 41 " --> pdb=" O ALA G 37 " (cutoff:3.500A) Processing helix chain 'H' and resid 3 through 5 No H-bonds generated for 'chain 'H' and resid 3 through 5' Processing helix chain 'H' and resid 6 through 11 Processing helix chain 'H' and resid 17 through 42 removed outlier: 4.377A pdb=" N THR H 23 " --> pdb=" O THR H 19 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N THR H 30 " --> pdb=" O THR H 26 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N THR H 41 " --> pdb=" O ALA H 37 " (cutoff:3.500A) Processing helix chain 'I' and resid 3 through 5 No H-bonds generated for 'chain 'I' and resid 3 through 5' Processing helix chain 'I' and resid 6 through 11 Processing helix chain 'I' and resid 17 through 42 removed outlier: 4.378A pdb=" N THR I 23 " --> pdb=" O THR I 19 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N THR I 30 " --> pdb=" O THR I 26 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N THR I 41 " --> pdb=" O ALA I 37 " (cutoff:3.500A) Processing helix chain 'J' and resid 3 through 5 No H-bonds generated for 'chain 'J' and resid 3 through 5' Processing helix chain 'J' and resid 6 through 11 Processing helix chain 'J' and resid 17 through 42 removed outlier: 4.378A pdb=" N THR J 23 " --> pdb=" O THR J 19 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N THR J 30 " --> pdb=" O THR J 26 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N THR J 41 " --> pdb=" O ALA J 37 " (cutoff:3.500A) 210 hydrogen bonds defined for protein. 630 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: 0.75 Time building geometry restraints manager: 1.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.29: 480 1.29 - 1.35: 480 1.35 - 1.42: 140 1.42 - 1.48: 550 1.48 - 1.54: 1420 Bond restraints: 3070 Sorted by residual: bond pdb=" CA ALA E 38 " pdb=" C ALA E 38 " ideal model delta sigma weight residual 1.524 1.516 0.009 1.29e-02 6.01e+03 4.38e-01 bond pdb=" CA ALA A 38 " pdb=" C ALA A 38 " ideal model delta sigma weight residual 1.524 1.516 0.008 1.29e-02 6.01e+03 4.00e-01 bond pdb=" CA ALA C 38 " pdb=" C ALA C 38 " ideal model delta sigma weight residual 1.524 1.516 0.008 1.29e-02 6.01e+03 3.96e-01 bond pdb=" CA ALA I 38 " pdb=" C ALA I 38 " ideal model delta sigma weight residual 1.524 1.516 0.008 1.29e-02 6.01e+03 3.85e-01 bond pdb=" N ALA F 38 " pdb=" CA ALA F 38 " ideal model delta sigma weight residual 1.459 1.451 0.008 1.24e-02 6.50e+03 3.84e-01 ... (remaining 3065 not shown) Histogram of bond angle deviations from ideal: 108.49 - 111.59: 1698 111.59 - 114.70: 422 114.70 - 117.80: 325 117.80 - 120.90: 1006 120.90 - 124.01: 769 Bond angle restraints: 4220 Sorted by residual: angle pdb=" N ILE G 4 " pdb=" CA ILE G 4 " pdb=" C ILE G 4 " ideal model delta sigma weight residual 109.34 112.59 -3.25 2.08e+00 2.31e-01 2.44e+00 angle pdb=" N ILE F 4 " pdb=" CA ILE F 4 " pdb=" C ILE F 4 " ideal model delta sigma weight residual 109.34 112.59 -3.25 2.08e+00 2.31e-01 2.43e+00 angle pdb=" N ILE A 4 " pdb=" CA ILE A 4 " pdb=" C ILE A 4 " ideal model delta sigma weight residual 109.34 112.58 -3.24 2.08e+00 2.31e-01 2.43e+00 angle pdb=" N ILE H 4 " pdb=" CA ILE H 4 " pdb=" C ILE H 4 " ideal model delta sigma weight residual 109.34 112.58 -3.24 2.08e+00 2.31e-01 2.42e+00 angle pdb=" N ILE B 4 " pdb=" CA ILE B 4 " pdb=" C ILE B 4 " ideal model delta sigma weight residual 109.34 112.56 -3.22 2.08e+00 2.31e-01 2.40e+00 ... (remaining 4215 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 9.83: 1500 9.83 - 19.66: 140 19.66 - 29.49: 70 29.49 - 39.32: 30 39.32 - 49.16: 30 Dihedral angle restraints: 1770 sinusoidal: 500 harmonic: 1270 Sorted by residual: dihedral pdb=" N ILE A 4 " pdb=" CA ILE A 4 " pdb=" CB ILE A 4 " pdb=" CG1 ILE A 4 " ideal model delta sinusoidal sigma weight residual -60.00 -10.84 -49.16 3 1.50e+01 4.44e-03 8.74e+00 dihedral pdb=" N ILE B 4 " pdb=" CA ILE B 4 " pdb=" CB ILE B 4 " pdb=" CG1 ILE B 4 " ideal model delta sinusoidal sigma weight residual -60.00 -10.85 -49.15 3 1.50e+01 4.44e-03 8.74e+00 dihedral pdb=" N ILE I 4 " pdb=" CA ILE I 4 " pdb=" CB ILE I 4 " pdb=" CG1 ILE I 4 " ideal model delta sinusoidal sigma weight residual -60.00 -10.90 -49.10 3 1.50e+01 4.44e-03 8.73e+00 ... (remaining 1767 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.021: 282 0.021 - 0.041: 173 0.041 - 0.062: 95 0.062 - 0.083: 50 0.083 - 0.103: 40 Chirality restraints: 640 Sorted by residual: chirality pdb=" CA THR F 30 " pdb=" N THR F 30 " pdb=" C THR F 30 " pdb=" CB THR F 30 " both_signs ideal model delta sigma weight residual False 2.53 2.42 0.10 2.00e-01 2.50e+01 2.67e-01 chirality pdb=" CA THR A 30 " pdb=" N THR A 30 " pdb=" C THR A 30 " pdb=" CB THR A 30 " both_signs ideal model delta sigma weight residual False 2.53 2.42 0.10 2.00e-01 2.50e+01 2.59e-01 chirality pdb=" CA THR J 30 " pdb=" N THR J 30 " pdb=" C THR J 30 " pdb=" CB THR J 30 " both_signs ideal model delta sigma weight residual False 2.53 2.42 0.10 2.00e-01 2.50e+01 2.57e-01 ... (remaining 637 not shown) Planarity restraints: 490 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY F 25 " 0.008 2.00e-02 2.50e+03 1.52e-02 2.31e+00 pdb=" C GLY F 25 " -0.026 2.00e-02 2.50e+03 pdb=" O GLY F 25 " 0.010 2.00e-02 2.50e+03 pdb=" N THR F 26 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY J 25 " 0.008 2.00e-02 2.50e+03 1.51e-02 2.28e+00 pdb=" C GLY J 25 " -0.026 2.00e-02 2.50e+03 pdb=" O GLY J 25 " 0.010 2.00e-02 2.50e+03 pdb=" N THR J 26 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY G 25 " -0.008 2.00e-02 2.50e+03 1.51e-02 2.28e+00 pdb=" C GLY G 25 " 0.026 2.00e-02 2.50e+03 pdb=" O GLY G 25 " -0.010 2.00e-02 2.50e+03 pdb=" N THR G 26 " -0.009 2.00e-02 2.50e+03 ... (remaining 487 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.74: 509 2.74 - 3.28: 3380 3.28 - 3.82: 5155 3.82 - 4.36: 5996 4.36 - 4.90: 9519 Nonbonded interactions: 24559 Sorted by model distance: nonbonded pdb=" O ARG D 29 " pdb=" OG1 THR D 33 " model vdw 2.206 2.440 nonbonded pdb=" O ARG A 29 " pdb=" OG1 THR A 33 " model vdw 2.206 2.440 nonbonded pdb=" O ARG J 29 " pdb=" OG1 THR J 33 " model vdw 2.206 2.440 nonbonded pdb=" O ARG H 29 " pdb=" OG1 THR H 33 " model vdw 2.207 2.440 nonbonded pdb=" O ARG B 29 " pdb=" OG1 THR B 33 " model vdw 2.207 2.440 ... (remaining 24554 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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 6.820 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 13.900 Find NCS groups from input model: 0.220 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:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.018 3070 Z= 0.239 Angle : 0.609 3.251 4220 Z= 0.377 Chirality : 0.040 0.103 640 Planarity : 0.003 0.015 490 Dihedral : 13.638 49.155 950 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 12.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 3.33 % Allowed : 10.00 % Favored : 86.67 % 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: -5.99 (0.23), residues: 430 helix: -3.55 (0.17), residues: 340 sheet: None (None), residues: 0 loop : -4.60 (0.29), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.002 0.001 PHE B 32 TYR 0.003 0.001 TYR C 6 ARG 0.002 0.001 ARG G 29 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 860 Ramachandran restraints generated. 430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 860 Ramachandran restraints generated. 430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 215 time to evaluate : 0.316 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 6 residues processed: 224 average time/residue: 0.1333 time to fit residues: 35.6805 Evaluate side-chains 221 residues out of total 300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 215 time to evaluate : 0.328 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0333 time to fit residues: 0.7573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 4.9990 chunk 30 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 20 optimal weight: 0.5980 chunk 31 optimal weight: 0.7980 chunk 12 optimal weight: 2.9990 chunk 19 optimal weight: 5.9990 chunk 23 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 27 ASN E 27 ASN G 27 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.2998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 3070 Z= 0.164 Angle : 0.550 5.031 4220 Z= 0.301 Chirality : 0.038 0.118 640 Planarity : 0.004 0.038 490 Dihedral : 4.746 12.053 460 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 14.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 10.33 % Allowed : 37.00 % Favored : 52.67 % 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: -4.87 (0.30), residues: 430 helix: -2.82 (0.22), residues: 340 sheet: None (None), residues: 0 loop : -3.93 (0.36), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.002 0.000 PHE I 32 TYR 0.008 0.002 TYR C 6 ARG 0.007 0.001 ARG E 29 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 860 Ramachandran restraints generated. 430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 860 Ramachandran restraints generated. 430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 204 time to evaluate : 0.324 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 31 outliers final: 25 residues processed: 208 average time/residue: 0.1336 time to fit residues: 33.0285 Evaluate side-chains 232 residues out of total 300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 207 time to evaluate : 0.279 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 0 residues processed: 25 average time/residue: 0.0292 time to fit residues: 1.6354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 30 optimal weight: 3.9990 chunk 24 optimal weight: 0.5980 chunk 10 optimal weight: 0.8980 chunk 36 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 12 optimal weight: 4.9990 chunk 29 optimal weight: 3.9990 chunk 35 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 27 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.3384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3070 Z= 0.211 Angle : 0.589 6.511 4220 Z= 0.329 Chirality : 0.040 0.105 640 Planarity : 0.005 0.051 490 Dihedral : 4.748 12.910 460 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 15.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 6.00 % Allowed : 41.67 % Favored : 52.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.78 (0.30), residues: 430 helix: -2.83 (0.22), residues: 340 sheet: None (None), residues: 0 loop : -3.53 (0.41), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.002 0.000 PHE B 32 TYR 0.005 0.001 TYR C 6 ARG 0.012 0.002 ARG B 29 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 860 Ramachandran restraints generated. 430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 860 Ramachandran restraints generated. 430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 211 time to evaluate : 0.285 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 11 residues processed: 215 average time/residue: 0.1298 time to fit residues: 33.3537 Evaluate side-chains 222 residues out of total 300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 211 time to evaluate : 0.303 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.0317 time to fit residues: 0.9899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 4 optimal weight: 0.7980 chunk 17 optimal weight: 4.9990 chunk 24 optimal weight: 4.9990 chunk 36 optimal weight: 0.5980 chunk 38 optimal weight: 0.8980 chunk 19 optimal weight: 0.9990 chunk 34 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 chunk 21 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 27 ASN E 27 ASN J 27 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.3850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3070 Z= 0.188 Angle : 0.593 6.006 4220 Z= 0.323 Chirality : 0.040 0.117 640 Planarity : 0.005 0.073 490 Dihedral : 4.625 15.666 460 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 14.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 8.67 % Allowed : 42.67 % Favored : 48.67 % 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: -4.54 (0.30), residues: 430 helix: -2.68 (0.22), residues: 340 sheet: None (None), residues: 0 loop : -3.35 (0.41), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.003 0.001 PHE C 32 TYR 0.004 0.001 TYR D 6 ARG 0.013 0.001 ARG B 29 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 860 Ramachandran restraints generated. 430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 860 Ramachandran restraints generated. 430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 208 time to evaluate : 0.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 21 residues processed: 213 average time/residue: 0.1351 time to fit residues: 34.5015 Evaluate side-chains 229 residues out of total 300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 208 time to evaluate : 0.310 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.0501 time to fit residues: 1.9195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 28 optimal weight: 5.9990 chunk 15 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 19 optimal weight: 0.7980 chunk 34 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 13 optimal weight: 0.4980 chunk 7 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 27 ASN D 27 ASN E 27 ASN F 27 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.4216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3070 Z= 0.226 Angle : 0.623 7.731 4220 Z= 0.338 Chirality : 0.042 0.181 640 Planarity : 0.006 0.074 490 Dihedral : 4.737 15.304 460 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 15.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 6.33 % Allowed : 40.33 % Favored : 53.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.66 (0.30), residues: 430 helix: -2.81 (0.21), residues: 340 sheet: None (None), residues: 0 loop : -3.18 (0.45), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.003 0.001 PHE D 32 TYR 0.005 0.001 TYR D 6 ARG 0.005 0.001 ARG B 29 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 860 Ramachandran restraints generated. 430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 860 Ramachandran restraints generated. 430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 206 time to evaluate : 0.393 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 13 residues processed: 212 average time/residue: 0.1327 time to fit residues: 33.6171 Evaluate side-chains 219 residues out of total 300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 206 time to evaluate : 0.321 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.0308 time to fit residues: 1.1059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 9 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 chunk 3 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 37 optimal weight: 0.2980 chunk 4 optimal weight: 0.2980 chunk 22 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 27 ASN D 27 ASN E 27 ASN F 27 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.4479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3070 Z= 0.192 Angle : 0.641 6.568 4220 Z= 0.343 Chirality : 0.040 0.110 640 Planarity : 0.004 0.049 490 Dihedral : 4.494 14.732 460 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 12.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 5.33 % Allowed : 44.67 % Favored : 50.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.38 (0.31), residues: 430 helix: -2.66 (0.22), residues: 340 sheet: None (None), residues: 0 loop : -2.85 (0.49), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.006 0.001 PHE D 32 TYR 0.006 0.001 TYR D 6 ARG 0.004 0.001 ARG G 29 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 860 Ramachandran restraints generated. 430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 860 Ramachandran restraints generated. 430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 198 time to evaluate : 0.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 13 residues processed: 200 average time/residue: 0.1410 time to fit residues: 33.5119 Evaluate side-chains 210 residues out of total 300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 197 time to evaluate : 0.331 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.0318 time to fit residues: 1.1335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 21 optimal weight: 0.0980 chunk 32 optimal weight: 0.6980 chunk 38 optimal weight: 3.9990 chunk 24 optimal weight: 5.9990 chunk 23 optimal weight: 0.7980 chunk 17 optimal weight: 7.9990 chunk 15 optimal weight: 0.9980 chunk 11 optimal weight: 4.9990 chunk 7 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 27 ASN D 27 ASN E 27 ASN F 27 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.4852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3070 Z= 0.203 Angle : 0.645 6.450 4220 Z= 0.342 Chirality : 0.042 0.263 640 Planarity : 0.004 0.048 490 Dihedral : 4.455 16.748 460 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 14.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 4.67 % Allowed : 42.33 % Favored : 53.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.30 (0.31), residues: 430 helix: -2.60 (0.22), residues: 340 sheet: None (None), residues: 0 loop : -2.82 (0.49), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.011 0.001 PHE D 32 TYR 0.007 0.001 TYR G 6 ARG 0.003 0.001 ARG D 29 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 860 Ramachandran restraints generated. 430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 860 Ramachandran restraints generated. 430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 186 time to evaluate : 0.314 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 9 residues processed: 188 average time/residue: 0.1478 time to fit residues: 32.9918 Evaluate side-chains 195 residues out of total 300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 186 time to evaluate : 0.313 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0329 time to fit residues: 0.9172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 3 optimal weight: 3.9990 chunk 30 optimal weight: 0.8980 chunk 35 optimal weight: 0.8980 chunk 36 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 21 optimal weight: 0.3980 chunk 15 optimal weight: 0.6980 chunk 28 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 27 ASN D 27 ASN E 27 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.4889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3070 Z= 0.215 Angle : 0.668 6.472 4220 Z= 0.356 Chirality : 0.042 0.169 640 Planarity : 0.005 0.047 490 Dihedral : 4.544 14.685 460 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 15.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 3.67 % Allowed : 45.00 % Favored : 51.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.85 (0.30), residues: 430 helix: -2.96 (0.21), residues: 370 sheet: None (None), residues: 0 loop : -2.85 (0.52), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.007 0.001 PHE D 32 TYR 0.008 0.001 TYR G 6 ARG 0.006 0.001 ARG D 29 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 860 Ramachandran restraints generated. 430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 860 Ramachandran restraints generated. 430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 195 time to evaluate : 0.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 9 residues processed: 196 average time/residue: 0.1435 time to fit residues: 33.3461 Evaluate side-chains 203 residues out of total 300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 194 time to evaluate : 0.317 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0310 time to fit residues: 0.8771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 37 optimal weight: 7.9990 chunk 23 optimal weight: 0.8980 chunk 18 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 24 optimal weight: 0.6980 chunk 19 optimal weight: 6.9990 chunk 25 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: C 27 ASN D 27 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.4817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 3070 Z= 0.268 Angle : 0.712 7.987 4220 Z= 0.384 Chirality : 0.045 0.187 640 Planarity : 0.005 0.061 490 Dihedral : 4.875 15.917 460 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 17.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 3.33 % Allowed : 44.67 % Favored : 52.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.25 (0.28), residues: 430 helix: -3.25 (0.19), residues: 370 sheet: None (None), residues: 0 loop : -2.76 (0.51), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.009 0.001 PHE E 32 TYR 0.009 0.001 TYR G 6 ARG 0.010 0.001 ARG G 29 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 860 Ramachandran restraints generated. 430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 860 Ramachandran restraints generated. 430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 203 time to evaluate : 0.320 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 8 residues processed: 205 average time/residue: 0.1368 time to fit residues: 33.4017 Evaluate side-chains 209 residues out of total 300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 201 time to evaluate : 0.318 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0306 time to fit residues: 0.8266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 0.0870 chunk 9 optimal weight: 2.9990 chunk 29 optimal weight: 5.9990 chunk 4 optimal weight: 8.9990 chunk 8 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 13 optimal weight: 5.9990 chunk 32 optimal weight: 0.8980 chunk 5 optimal weight: 10.0000 chunk 27 optimal weight: 0.9980 chunk 1 optimal weight: 0.9980 overall best weight: 1.1960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 27 ASN D 27 ASN E 27 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.4979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3070 Z= 0.244 Angle : 0.746 11.408 4220 Z= 0.385 Chirality : 0.045 0.242 640 Planarity : 0.006 0.078 490 Dihedral : 4.829 17.221 460 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 16.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 1.00 % Allowed : 49.00 % Favored : 50.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.09 (0.29), residues: 430 helix: -3.14 (0.20), residues: 370 sheet: None (None), residues: 0 loop : -2.80 (0.50), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.005 0.001 PHE D 32 TYR 0.009 0.001 TYR G 6 ARG 0.006 0.001 ARG A 29 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 860 Ramachandran restraints generated. 430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 860 Ramachandran restraints generated. 430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 197 time to evaluate : 0.291 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 197 average time/residue: 0.1400 time to fit residues: 32.6892 Evaluate side-chains 198 residues out of total 300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 196 time to evaluate : 0.311 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0311 time to fit residues: 0.4973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 22 optimal weight: 0.9980 chunk 36 optimal weight: 0.8980 chunk 21 optimal weight: 5.9990 chunk 27 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 24 optimal weight: 0.7980 chunk 23 optimal weight: 0.8980 chunk 15 optimal weight: 0.7980 chunk 14 optimal weight: 2.9990 chunk 39 optimal weight: 5.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 27 ASN D 27 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.105396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.095432 restraints weight = 5699.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.097779 restraints weight = 2746.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.099231 restraints weight = 1602.205| |-----------------------------------------------------------------------------| r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.5166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3070 Z= 0.214 Angle : 0.710 10.146 4220 Z= 0.366 Chirality : 0.043 0.222 640 Planarity : 0.005 0.060 490 Dihedral : 4.662 16.965 460 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 14.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 3.33 % Allowed : 45.33 % Favored : 51.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.80 (0.30), residues: 430 helix: -2.95 (0.21), residues: 370 sheet: None (None), residues: 0 loop : -2.65 (0.52), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.010 0.001 PHE E 32 TYR 0.009 0.001 TYR G 6 ARG 0.006 0.001 ARG D 29 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1167.27 seconds wall clock time: 21 minutes 56.21 seconds (1316.21 seconds total)