Starting phenix.real_space_refine on Sun Mar 10 20:27:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sza_40905/03_2024/8sza_40905_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sza_40905/03_2024/8sza_40905.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sza_40905/03_2024/8sza_40905.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sza_40905/03_2024/8sza_40905.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sza_40905/03_2024/8sza_40905_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sza_40905/03_2024/8sza_40905_updated.pdb" } resolution = 2.75 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= 0.025 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 12 5.16 5 C 3258 2.51 5 N 726 2.21 5 O 804 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 69": "OE1" <-> "OE2" Residue "A PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 116": "OD1" <-> "OD2" Residue "C TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 49": "OE1" <-> "OE2" Residue "D ASP 53": "OD1" <-> "OD2" Residue "E ASP 53": "OD1" <-> "OD2" Residue "E PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 49": "OE1" <-> "OE2" Residue "F ASP 53": "OD1" <-> "OD2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 4800 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 772 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 3, 'TRANS': 97} Chain: "B" Number of atoms: 772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 772 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 3, 'TRANS': 97} Chain: "C" Number of atoms: 772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 772 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 3, 'TRANS': 97} Chain: "D" Number of atoms: 772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 772 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 3, 'TRANS': 97} Chain: "E" Number of atoms: 772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 772 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 3, 'TRANS': 97} Chain: "F" Number of atoms: 772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 772 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 3, 'TRANS': 97} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 56 Unusual residues: {'CLR': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.02, per 1000 atoms: 0.63 Number of scatterers: 4800 At special positions: 0 Unit cell: (56.76, 70.62, 94.38, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 12 16.00 O 804 8.00 N 726 7.00 C 3258 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: 1.86 Conformation dependent library (CDL) restraints added in 847.0 milliseconds 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1164 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 25 helices and 0 sheets defined 82.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.78 Creating SS restraints... Processing helix chain 'A' and resid 40 through 51 removed outlier: 3.965A pdb=" N MET A 51 " --> pdb=" O ALA A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 70 Processing helix chain 'A' and resid 77 through 107 removed outlier: 4.120A pdb=" N LYS A 103 " --> pdb=" O ILE A 99 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N TYR A 104 " --> pdb=" O PHE A 100 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N LEU A 106 " --> pdb=" O VAL A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 138 Processing helix chain 'B' and resid 40 through 51 removed outlier: 3.953A pdb=" N MET B 51 " --> pdb=" O ALA B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 70 Processing helix chain 'B' and resid 77 through 106 removed outlier: 4.175A pdb=" N LYS B 103 " --> pdb=" O ILE B 99 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N TYR B 104 " --> pdb=" O PHE B 100 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ASP B 105 " --> pdb=" O LEU B 101 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LEU B 106 " --> pdb=" O VAL B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 138 Processing helix chain 'C' and resid 40 through 51 removed outlier: 3.506A pdb=" N SER C 50 " --> pdb=" O SER C 46 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N MET C 51 " --> pdb=" O ALA C 47 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 70 Processing helix chain 'C' and resid 77 through 99 Processing helix chain 'C' and resid 112 through 138 Processing helix chain 'D' and resid 40 through 51 removed outlier: 4.065A pdb=" N MET D 51 " --> pdb=" O ALA D 47 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 70 Processing helix chain 'D' and resid 77 through 106 removed outlier: 3.512A pdb=" N VAL D 102 " --> pdb=" O LEU D 98 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N LYS D 103 " --> pdb=" O ILE D 99 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N TYR D 104 " --> pdb=" O PHE D 100 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LEU D 106 " --> pdb=" O VAL D 102 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 138 removed outlier: 3.643A pdb=" N PHE D 135 " --> pdb=" O VAL D 131 " (cutoff:3.500A) Processing helix chain 'E' and resid 40 through 51 removed outlier: 4.013A pdb=" N MET E 51 " --> pdb=" O ALA E 47 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 70 Processing helix chain 'E' and resid 77 through 102 Processing helix chain 'E' and resid 104 through 107 No H-bonds generated for 'chain 'E' and resid 104 through 107' Processing helix chain 'E' and resid 112 through 138 Processing helix chain 'F' and resid 40 through 51 removed outlier: 4.272A pdb=" N MET F 51 " --> pdb=" O ALA F 47 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 70 Processing helix chain 'F' and resid 77 through 102 Processing helix chain 'F' and resid 112 through 138 381 hydrogen bonds defined for protein. 1143 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.37 Time building geometry restraints manager: 2.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 1416 1.35 - 1.46: 1057 1.46 - 1.58: 2405 1.58 - 1.70: 0 1.70 - 1.82: 24 Bond restraints: 4902 Sorted by residual: bond pdb=" CB GLU A 69 " pdb=" CG GLU A 69 " ideal model delta sigma weight residual 1.520 1.563 -0.043 3.00e-02 1.11e+03 2.06e+00 bond pdb=" CA PHE C 74 " pdb=" CB PHE C 74 " ideal model delta sigma weight residual 1.528 1.507 0.021 1.58e-02 4.01e+03 1.70e+00 bond pdb=" CD2 HIS F 112 " pdb=" NE2 HIS F 112 " ideal model delta sigma weight residual 1.374 1.360 0.014 1.10e-02 8.26e+03 1.61e+00 bond pdb=" CA HIS F 112 " pdb=" CB HIS F 112 " ideal model delta sigma weight residual 1.528 1.510 0.019 1.59e-02 3.96e+03 1.39e+00 bond pdb=" CG HIS F 112 " pdb=" ND1 HIS F 112 " ideal model delta sigma weight residual 1.378 1.390 -0.012 1.10e-02 8.26e+03 1.28e+00 ... (remaining 4897 not shown) Histogram of bond angle deviations from ideal: 99.31 - 105.72: 97 105.72 - 112.14: 2731 112.14 - 118.55: 1316 118.55 - 124.97: 2528 124.97 - 131.39: 36 Bond angle restraints: 6708 Sorted by residual: angle pdb=" CB MET A 51 " pdb=" CG MET A 51 " pdb=" SD MET A 51 " ideal model delta sigma weight residual 112.70 123.47 -10.77 3.00e+00 1.11e-01 1.29e+01 angle pdb=" CA MET A 58 " pdb=" CB MET A 58 " pdb=" CG MET A 58 " ideal model delta sigma weight residual 114.10 120.87 -6.77 2.00e+00 2.50e-01 1.14e+01 angle pdb=" CA GLU A 69 " pdb=" CB GLU A 69 " pdb=" CG GLU A 69 " ideal model delta sigma weight residual 114.10 120.83 -6.73 2.00e+00 2.50e-01 1.13e+01 angle pdb=" C TYR D 77 " pdb=" N VAL D 78 " pdb=" CA VAL D 78 " ideal model delta sigma weight residual 120.33 122.84 -2.51 8.00e-01 1.56e+00 9.83e+00 angle pdb=" CB GLU A 69 " pdb=" CG GLU A 69 " pdb=" CD GLU A 69 " ideal model delta sigma weight residual 112.60 117.81 -5.21 1.70e+00 3.46e-01 9.41e+00 ... (remaining 6703 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.55: 2792 16.55 - 33.09: 284 33.09 - 49.64: 88 49.64 - 66.19: 27 66.19 - 82.73: 1 Dihedral angle restraints: 3192 sinusoidal: 1410 harmonic: 1782 Sorted by residual: dihedral pdb=" CG LYS B 65 " pdb=" CD LYS B 65 " pdb=" CE LYS B 65 " pdb=" NZ LYS B 65 " ideal model delta sinusoidal sigma weight residual -60.00 -2.88 -57.12 3 1.50e+01 4.44e-03 9.43e+00 dihedral pdb=" CG LYS B 103 " pdb=" CD LYS B 103 " pdb=" CE LYS B 103 " pdb=" NZ LYS B 103 " ideal model delta sinusoidal sigma weight residual 180.00 122.94 57.06 3 1.50e+01 4.44e-03 9.43e+00 dihedral pdb=" N MET E 51 " pdb=" CA MET E 51 " pdb=" CB MET E 51 " pdb=" CG MET E 51 " ideal model delta sinusoidal sigma weight residual -180.00 -123.30 -56.70 3 1.50e+01 4.44e-03 9.41e+00 ... (remaining 3189 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.021: 454 0.021 - 0.042: 244 0.042 - 0.063: 109 0.063 - 0.084: 45 0.084 - 0.104: 18 Chirality restraints: 870 Sorted by residual: chirality pdb=" CB VAL A 67 " pdb=" CA VAL A 67 " pdb=" CG1 VAL A 67 " pdb=" CG2 VAL A 67 " both_signs ideal model delta sigma weight residual False -2.63 -2.52 -0.10 2.00e-01 2.50e+01 2.73e-01 chirality pdb=" CA PRO F 79 " pdb=" N PRO F 79 " pdb=" C PRO F 79 " pdb=" CB PRO F 79 " both_signs ideal model delta sigma weight residual False 2.72 2.62 0.10 2.00e-01 2.50e+01 2.48e-01 chirality pdb=" CA PRO C 79 " pdb=" N PRO C 79 " pdb=" C PRO C 79 " pdb=" CB PRO C 79 " both_signs ideal model delta sigma weight residual False 2.72 2.62 0.10 2.00e-01 2.50e+01 2.42e-01 ... (remaining 867 not shown) Planarity restraints: 780 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 127 " -0.013 2.00e-02 2.50e+03 1.72e-02 5.18e+00 pdb=" CG PHE A 127 " 0.039 2.00e-02 2.50e+03 pdb=" CD1 PHE A 127 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 PHE A 127 " -0.015 2.00e-02 2.50e+03 pdb=" CE1 PHE A 127 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE A 127 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE A 127 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU A 69 " -0.010 2.00e-02 2.50e+03 2.12e-02 4.50e+00 pdb=" CD GLU A 69 " 0.037 2.00e-02 2.50e+03 pdb=" OE1 GLU A 69 " -0.013 2.00e-02 2.50e+03 pdb=" OE2 GLU A 69 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP F 53 " -0.006 2.00e-02 2.50e+03 1.29e-02 1.66e+00 pdb=" CG ASP F 53 " 0.022 2.00e-02 2.50e+03 pdb=" OD1 ASP F 53 " -0.008 2.00e-02 2.50e+03 pdb=" OD2 ASP F 53 " -0.008 2.00e-02 2.50e+03 ... (remaining 777 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 184 2.73 - 3.27: 5230 3.27 - 3.81: 7815 3.81 - 4.36: 8986 4.36 - 4.90: 15080 Nonbonded interactions: 37295 Sorted by model distance: nonbonded pdb=" O MET D 58 " pdb=" OG SER D 62 " model vdw 2.185 2.440 nonbonded pdb=" OH TYR F 104 " pdb=" O1 CLR F 201 " model vdw 2.196 2.440 nonbonded pdb=" O MET E 58 " pdb=" OG SER E 62 " model vdw 2.225 2.440 nonbonded pdb=" OD1 ASN D 120 " pdb=" NZ LYS E 103 " model vdw 2.351 2.520 nonbonded pdb=" O MET F 58 " pdb=" OG SER F 62 " model vdw 2.414 2.440 ... (remaining 37290 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' and resid 39 through 139) selection = (chain 'C' and resid 39 through 139) selection = (chain 'D' and resid 39 through 139) selection = (chain 'E' and resid 39 through 139) selection = (chain 'F' and resid 39 through 139) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.940 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: 9.570 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 17.320 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.030 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:14.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 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 : 0.003 0.043 4902 Z= 0.211 Angle : 0.652 10.766 6708 Z= 0.325 Chirality : 0.033 0.104 870 Planarity : 0.002 0.022 780 Dihedral : 15.140 82.732 2028 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Rotamer: Outliers : 0.98 % Allowed : 20.98 % Favored : 78.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.12 (0.35), residues: 594 helix: 1.96 (0.23), residues: 492 sheet: None (None), residues: 0 loop : -1.39 (0.67), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS B 112 PHE 0.039 0.001 PHE A 127 TYR 0.009 0.001 TYR B 77 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 87 time to evaluate : 0.484 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 44 LYS cc_start: 0.6964 (mmtt) cc_final: 0.5977 (tmtt) outliers start: 5 outliers final: 5 residues processed: 90 average time/residue: 0.7270 time to fit residues: 69.4116 Evaluate side-chains 89 residues out of total 510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 84 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 54 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 50 optimal weight: 1.9990 chunk 45 optimal weight: 0.6980 chunk 25 optimal weight: 3.9990 chunk 15 optimal weight: 0.8980 chunk 30 optimal weight: 10.0000 chunk 24 optimal weight: 0.9980 chunk 47 optimal weight: 10.0000 chunk 18 optimal weight: 0.9990 chunk 28 optimal weight: 0.8980 chunk 35 optimal weight: 0.5980 chunk 54 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.1520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4902 Z= 0.188 Angle : 0.543 7.010 6708 Z= 0.271 Chirality : 0.036 0.143 870 Planarity : 0.003 0.016 780 Dihedral : 9.500 50.693 1017 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Rotamer: Outliers : 1.96 % Allowed : 20.00 % Favored : 78.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.44 (0.35), residues: 594 helix: 2.14 (0.23), residues: 522 sheet: None (None), residues: 0 loop : -2.48 (0.71), residues: 72 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 112 PHE 0.019 0.002 PHE F 127 TYR 0.012 0.001 TYR D 41 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 93 time to evaluate : 0.553 Fit side-chains REVERT: A 58 MET cc_start: 0.7997 (mpt) cc_final: 0.7691 (mpt) REVERT: B 58 MET cc_start: 0.7315 (mtp) cc_final: 0.7067 (mtm) REVERT: D 44 LYS cc_start: 0.7098 (mmtt) cc_final: 0.6091 (tmtt) outliers start: 10 outliers final: 5 residues processed: 97 average time/residue: 0.6802 time to fit residues: 70.3322 Evaluate side-chains 89 residues out of total 510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 84 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain F residue 137 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 30 optimal weight: 10.0000 chunk 16 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 chunk 37 optimal weight: 5.9990 chunk 15 optimal weight: 0.7980 chunk 54 optimal weight: 0.8980 chunk 58 optimal weight: 0.7980 chunk 48 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.1749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4902 Z= 0.191 Angle : 0.519 6.921 6708 Z= 0.256 Chirality : 0.036 0.117 870 Planarity : 0.002 0.016 780 Dihedral : 9.396 50.327 1008 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 3.14 % Allowed : 20.20 % Favored : 76.67 % 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: 2.42 (0.36), residues: 594 helix: 2.04 (0.23), residues: 534 sheet: None (None), residues: 0 loop : -2.46 (0.82), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS F 112 PHE 0.021 0.002 PHE C 127 TYR 0.015 0.001 TYR B 77 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 91 time to evaluate : 0.497 Fit side-chains revert: symmetry clash REVERT: A 58 MET cc_start: 0.7958 (mpt) cc_final: 0.7428 (mpt) REVERT: B 58 MET cc_start: 0.7350 (mtp) cc_final: 0.7073 (mtm) REVERT: D 44 LYS cc_start: 0.7067 (mmtt) cc_final: 0.5977 (tmtt) REVERT: D 101 LEU cc_start: 0.7865 (OUTLIER) cc_final: 0.7518 (tt) REVERT: E 88 LEU cc_start: 0.8300 (OUTLIER) cc_final: 0.7975 (tm) outliers start: 16 outliers final: 6 residues processed: 100 average time/residue: 0.6802 time to fit residues: 72.4348 Evaluate side-chains 91 residues out of total 510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 83 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain E residue 73 SER Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain F residue 62 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 41 optimal weight: 0.7980 chunk 28 optimal weight: 3.9990 chunk 6 optimal weight: 0.9990 chunk 26 optimal weight: 5.9990 chunk 36 optimal weight: 5.9990 chunk 54 optimal weight: 0.7980 chunk 57 optimal weight: 3.9990 chunk 51 optimal weight: 0.9980 chunk 15 optimal weight: 0.9980 chunk 48 optimal weight: 0.6980 chunk 32 optimal weight: 3.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 119 ASN ** B 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.1961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4902 Z= 0.191 Angle : 0.540 10.790 6708 Z= 0.262 Chirality : 0.036 0.105 870 Planarity : 0.002 0.017 780 Dihedral : 9.318 50.147 1008 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Rotamer: Outliers : 3.33 % Allowed : 21.37 % Favored : 75.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.56 (0.36), residues: 594 helix: 2.12 (0.23), residues: 528 sheet: None (None), residues: 0 loop : -1.93 (0.79), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS F 112 PHE 0.027 0.002 PHE A 127 TYR 0.006 0.001 TYR B 77 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 87 time to evaluate : 0.539 Fit side-chains revert: symmetry clash REVERT: A 58 MET cc_start: 0.7952 (mpt) cc_final: 0.7366 (mpt) REVERT: A 97 LEU cc_start: 0.7870 (OUTLIER) cc_final: 0.7418 (tt) REVERT: B 58 MET cc_start: 0.7422 (mtp) cc_final: 0.7140 (mtm) REVERT: D 44 LYS cc_start: 0.7055 (mmtt) cc_final: 0.5911 (tmtt) REVERT: D 101 LEU cc_start: 0.7848 (OUTLIER) cc_final: 0.7498 (tt) outliers start: 17 outliers final: 11 residues processed: 97 average time/residue: 0.6870 time to fit residues: 71.0599 Evaluate side-chains 96 residues out of total 510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 83 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 MET Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain E residue 73 SER Chi-restraints excluded: chain F residue 62 SER Chi-restraints excluded: chain F residue 137 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 0 optimal weight: 6.9990 chunk 43 optimal weight: 2.9990 chunk 23 optimal weight: 0.0770 chunk 49 optimal weight: 0.9980 chunk 40 optimal weight: 0.9980 chunk 29 optimal weight: 0.7980 chunk 52 optimal weight: 0.9980 chunk 14 optimal weight: 0.5980 chunk 19 optimal weight: 0.0020 chunk 11 optimal weight: 4.9990 chunk 34 optimal weight: 0.9980 overall best weight: 0.4946 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 60 ASN E 63 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.2133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 4902 Z= 0.154 Angle : 0.509 7.501 6708 Z= 0.247 Chirality : 0.034 0.101 870 Planarity : 0.002 0.016 780 Dihedral : 9.158 49.223 1008 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % Rotamer: Outliers : 2.75 % Allowed : 21.76 % Favored : 75.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.79 (0.36), residues: 594 helix: 2.26 (0.23), residues: 534 sheet: None (None), residues: 0 loop : -2.19 (0.87), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS F 112 PHE 0.023 0.001 PHE C 127 TYR 0.004 0.001 TYR E 104 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 90 time to evaluate : 0.530 Fit side-chains revert: symmetry clash REVERT: A 58 MET cc_start: 0.7812 (mpt) cc_final: 0.7391 (mpt) REVERT: A 97 LEU cc_start: 0.7831 (OUTLIER) cc_final: 0.7356 (tt) REVERT: B 58 MET cc_start: 0.7456 (mtp) cc_final: 0.7169 (mtm) REVERT: B 119 ASN cc_start: 0.8160 (m-40) cc_final: 0.7861 (m-40) REVERT: C 135 PHE cc_start: 0.8771 (m-80) cc_final: 0.8502 (m-80) REVERT: D 44 LYS cc_start: 0.7030 (mmtt) cc_final: 0.5858 (tmtt) REVERT: D 101 LEU cc_start: 0.7849 (OUTLIER) cc_final: 0.7477 (tt) outliers start: 14 outliers final: 8 residues processed: 98 average time/residue: 0.6655 time to fit residues: 69.6231 Evaluate side-chains 94 residues out of total 510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 84 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 MET Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain F residue 62 SER Chi-restraints excluded: chain F residue 137 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 14 optimal weight: 0.5980 chunk 58 optimal weight: 2.9990 chunk 48 optimal weight: 0.8980 chunk 26 optimal weight: 4.9990 chunk 4 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 30 optimal weight: 10.0000 chunk 55 optimal weight: 0.6980 chunk 6 optimal weight: 2.9990 chunk 33 optimal weight: 0.0170 chunk 42 optimal weight: 3.9990 overall best weight: 0.8420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.2300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4902 Z= 0.191 Angle : 0.530 6.810 6708 Z= 0.261 Chirality : 0.035 0.103 870 Planarity : 0.002 0.015 780 Dihedral : 9.158 49.379 1008 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Rotamer: Outliers : 2.94 % Allowed : 22.55 % Favored : 74.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.66 (0.36), residues: 594 helix: 2.17 (0.23), residues: 534 sheet: None (None), residues: 0 loop : -2.20 (0.87), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS B 112 PHE 0.029 0.002 PHE A 127 TYR 0.006 0.001 TYR E 104 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 91 time to evaluate : 0.532 Fit side-chains revert: symmetry clash REVERT: A 58 MET cc_start: 0.7766 (mpt) cc_final: 0.7475 (mpt) REVERT: A 97 LEU cc_start: 0.7870 (OUTLIER) cc_final: 0.7419 (tt) REVERT: B 58 MET cc_start: 0.7484 (mtp) cc_final: 0.7178 (mtm) REVERT: B 119 ASN cc_start: 0.8179 (m-40) cc_final: 0.7871 (m-40) REVERT: D 44 LYS cc_start: 0.7057 (mmtt) cc_final: 0.5808 (tmtt) REVERT: D 45 LYS cc_start: 0.8189 (OUTLIER) cc_final: 0.7980 (tttm) REVERT: D 101 LEU cc_start: 0.7857 (OUTLIER) cc_final: 0.7594 (tt) outliers start: 15 outliers final: 9 residues processed: 99 average time/residue: 0.7226 time to fit residues: 76.0033 Evaluate side-chains 96 residues out of total 510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 84 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain D residue 45 LYS Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain F residue 62 SER Chi-restraints excluded: chain F residue 137 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 32 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 57 optimal weight: 4.9990 chunk 36 optimal weight: 0.4980 chunk 35 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 34 optimal weight: 0.5980 chunk 17 optimal weight: 0.9980 chunk 11 optimal weight: 6.9990 chunk 39 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.2406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4902 Z= 0.184 Angle : 0.548 8.800 6708 Z= 0.270 Chirality : 0.035 0.105 870 Planarity : 0.002 0.017 780 Dihedral : 9.118 48.998 1008 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % Rotamer: Outliers : 2.94 % Allowed : 24.12 % Favored : 72.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.75 (0.36), residues: 594 helix: 2.25 (0.23), residues: 528 sheet: None (None), residues: 0 loop : -1.89 (0.83), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS F 112 PHE 0.024 0.002 PHE C 127 TYR 0.013 0.001 TYR B 77 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 88 time to evaluate : 0.522 Fit side-chains revert: symmetry clash REVERT: A 58 MET cc_start: 0.7723 (mpt) cc_final: 0.7503 (mpt) REVERT: A 97 LEU cc_start: 0.7858 (OUTLIER) cc_final: 0.7378 (tt) REVERT: A 127 PHE cc_start: 0.8091 (t80) cc_final: 0.7873 (t80) REVERT: B 58 MET cc_start: 0.7483 (mtp) cc_final: 0.7185 (mtm) REVERT: B 119 ASN cc_start: 0.8190 (m-40) cc_final: 0.7901 (m-40) REVERT: D 44 LYS cc_start: 0.7087 (mmtt) cc_final: 0.5810 (tmtt) REVERT: D 45 LYS cc_start: 0.8166 (OUTLIER) cc_final: 0.7963 (tttm) REVERT: D 101 LEU cc_start: 0.7917 (OUTLIER) cc_final: 0.7483 (tt) REVERT: F 69 GLU cc_start: 0.8206 (pt0) cc_final: 0.7999 (pt0) outliers start: 15 outliers final: 10 residues processed: 97 average time/residue: 0.6591 time to fit residues: 68.2532 Evaluate side-chains 98 residues out of total 510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 85 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 MET Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain D residue 45 LYS Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain F residue 62 SER Chi-restraints excluded: chain F residue 137 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 28 optimal weight: 3.9990 chunk 5 optimal weight: 0.4980 chunk 45 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 50 optimal weight: 0.6980 chunk 53 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 42 optimal weight: 6.9990 chunk 16 optimal weight: 0.9980 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.2486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 4902 Z= 0.265 Angle : 0.607 8.937 6708 Z= 0.297 Chirality : 0.038 0.127 870 Planarity : 0.002 0.018 780 Dihedral : 9.428 50.803 1008 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Rotamer: Outliers : 2.55 % Allowed : 24.51 % Favored : 72.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.29 (0.35), residues: 594 helix: 1.93 (0.23), residues: 528 sheet: None (None), residues: 0 loop : -1.91 (0.79), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS B 112 PHE 0.028 0.002 PHE F 127 TYR 0.012 0.001 TYR B 77 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 83 time to evaluate : 0.535 Fit side-chains revert: symmetry clash REVERT: A 58 MET cc_start: 0.7707 (OUTLIER) cc_final: 0.7455 (mpt) REVERT: A 97 LEU cc_start: 0.7947 (OUTLIER) cc_final: 0.7582 (tt) REVERT: B 58 MET cc_start: 0.7503 (mtp) cc_final: 0.7192 (mtm) REVERT: B 115 LEU cc_start: 0.7531 (OUTLIER) cc_final: 0.7184 (tm) REVERT: B 119 ASN cc_start: 0.8243 (m-40) cc_final: 0.7903 (m-40) REVERT: D 101 LEU cc_start: 0.7908 (OUTLIER) cc_final: 0.7548 (tt) REVERT: F 62 SER cc_start: 0.8013 (OUTLIER) cc_final: 0.7787 (p) outliers start: 13 outliers final: 6 residues processed: 90 average time/residue: 0.7071 time to fit residues: 67.9671 Evaluate side-chains 90 residues out of total 510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 79 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 MET Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain F residue 62 SER Chi-restraints excluded: chain F residue 137 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 48 optimal weight: 0.5980 chunk 50 optimal weight: 0.6980 chunk 53 optimal weight: 4.9990 chunk 35 optimal weight: 0.8980 chunk 56 optimal weight: 0.0270 chunk 34 optimal weight: 0.8980 chunk 27 optimal weight: 0.0010 chunk 39 optimal weight: 0.7980 chunk 59 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 47 optimal weight: 0.9980 overall best weight: 0.4244 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 120 ASN D 133 ASN F 107 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.2582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 4902 Z= 0.167 Angle : 0.555 9.291 6708 Z= 0.275 Chirality : 0.035 0.207 870 Planarity : 0.002 0.021 780 Dihedral : 9.115 48.304 1008 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Rotamer: Outliers : 2.55 % Allowed : 25.29 % 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: 2.76 (0.36), residues: 594 helix: 2.27 (0.23), residues: 528 sheet: None (None), residues: 0 loop : -2.00 (0.77), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS F 112 PHE 0.015 0.001 PHE B 74 TYR 0.008 0.001 TYR B 77 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 97 time to evaluate : 0.533 Fit side-chains revert: symmetry clash REVERT: A 97 LEU cc_start: 0.7842 (OUTLIER) cc_final: 0.7358 (tt) REVERT: B 58 MET cc_start: 0.7489 (mtp) cc_final: 0.7182 (mtm) REVERT: B 119 ASN cc_start: 0.8210 (m-40) cc_final: 0.7882 (m-40) REVERT: C 70 GLN cc_start: 0.8418 (tp-100) cc_final: 0.8132 (tp-100) REVERT: D 44 LYS cc_start: 0.7130 (mmtt) cc_final: 0.5814 (tmtt) REVERT: D 101 LEU cc_start: 0.7874 (OUTLIER) cc_final: 0.7472 (tt) outliers start: 13 outliers final: 8 residues processed: 102 average time/residue: 0.7147 time to fit residues: 77.5608 Evaluate side-chains 98 residues out of total 510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 88 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 MET Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain F residue 62 SER Chi-restraints excluded: chain F residue 137 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 4 optimal weight: 0.7980 chunk 36 optimal weight: 2.9990 chunk 29 optimal weight: 0.6980 chunk 37 optimal weight: 0.7980 chunk 50 optimal weight: 0.9980 chunk 14 optimal weight: 0.5980 chunk 43 optimal weight: 0.3980 chunk 7 optimal weight: 0.0770 chunk 13 optimal weight: 0.8980 chunk 47 optimal weight: 0.6980 chunk 19 optimal weight: 3.9990 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 120 ASN ** B 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.2629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 4902 Z= 0.176 Angle : 0.578 9.020 6708 Z= 0.287 Chirality : 0.035 0.192 870 Planarity : 0.002 0.021 780 Dihedral : 9.031 49.479 1008 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Rotamer: Outliers : 1.76 % Allowed : 26.47 % Favored : 71.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.73 (0.36), residues: 594 helix: 2.24 (0.23), residues: 528 sheet: None (None), residues: 0 loop : -1.94 (0.77), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS F 112 PHE 0.029 0.001 PHE F 127 TYR 0.025 0.001 TYR D 77 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 88 time to evaluate : 0.565 Fit side-chains revert: symmetry clash REVERT: A 51 MET cc_start: 0.7178 (mmp) cc_final: 0.6607 (mmt) REVERT: A 97 LEU cc_start: 0.7835 (OUTLIER) cc_final: 0.7379 (tt) REVERT: B 58 MET cc_start: 0.7471 (mtp) cc_final: 0.7162 (mtm) REVERT: B 119 ASN cc_start: 0.8240 (m-40) cc_final: 0.7930 (m-40) REVERT: C 70 GLN cc_start: 0.8436 (tp-100) cc_final: 0.8120 (tp-100) REVERT: D 44 LYS cc_start: 0.7130 (mmtt) cc_final: 0.5804 (tmtt) REVERT: D 101 LEU cc_start: 0.7872 (OUTLIER) cc_final: 0.7469 (tt) outliers start: 9 outliers final: 6 residues processed: 92 average time/residue: 0.6886 time to fit residues: 67.7278 Evaluate side-chains 91 residues out of total 510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 83 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain F residue 62 SER Chi-restraints excluded: chain F residue 137 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 48 optimal weight: 0.9990 chunk 6 optimal weight: 0.0770 chunk 8 optimal weight: 0.9990 chunk 41 optimal weight: 0.4980 chunk 2 optimal weight: 0.7980 chunk 34 optimal weight: 0.7980 chunk 54 optimal weight: 0.7980 chunk 32 optimal weight: 0.8980 chunk 40 optimal weight: 0.8980 chunk 1 optimal weight: 7.9990 chunk 38 optimal weight: 0.9990 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4555 r_free = 0.4555 target = 0.187633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.157149 restraints weight = 6478.745| |-----------------------------------------------------------------------------| r_work (start): 0.4255 rms_B_bonded: 2.47 r_work: 0.4145 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.4145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.2688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 4902 Z= 0.185 Angle : 0.579 8.886 6708 Z= 0.290 Chirality : 0.036 0.198 870 Planarity : 0.002 0.023 780 Dihedral : 8.980 49.779 1008 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Rotamer: Outliers : 2.16 % Allowed : 27.06 % Favored : 70.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.71 (0.36), residues: 594 helix: 2.30 (0.23), residues: 522 sheet: None (None), residues: 0 loop : -2.22 (0.72), residues: 72 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS B 112 PHE 0.039 0.002 PHE A 127 TYR 0.025 0.001 TYR D 77 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1859.94 seconds wall clock time: 33 minutes 54.57 seconds (2034.57 seconds total)