Starting phenix.real_space_refine on Thu Nov 14 07:34:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sx3_40825/11_2024/8sx3_40825.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sx3_40825/11_2024/8sx3_40825.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sx3_40825/11_2024/8sx3_40825.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sx3_40825/11_2024/8sx3_40825.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sx3_40825/11_2024/8sx3_40825.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sx3_40825/11_2024/8sx3_40825.cif" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.008 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 17 5.16 5 C 3059 2.51 5 N 816 2.21 5 O 924 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 4816 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 913 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 4, 'TRANS': 112} Chain: "B" Number of atoms: 821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 821 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 101} Chain: "C" Number of atoms: 1236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1236 Classifications: {'peptide': 154} Link IDs: {'PTRANS': 8, 'TRANS': 145} Chain: "H" Number of atoms: 1016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1016 Classifications: {'peptide': 129} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 121} Chain: "L" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 802 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 4, 'TRANS': 102} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 4.60, per 1000 atoms: 0.96 Number of scatterers: 4816 At special positions: 0 Unit cell: (55.825, 67.425, 122.525, 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 17 16.00 O 924 8.00 N 816 7.00 C 3059 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 97 " distance=2.04 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 88 " distance=2.05 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 98 " distance=2.03 Simple disulfide: pdb=" SG CYS L 21 " - pdb=" SG CYS L 86 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " NAG-ASN " NAG D 1 " - " ASN C 74 " Time building additional restraints: 1.35 Conformation dependent library (CDL) restraints added in 631.6 milliseconds 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1102 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 11 sheets defined 18.9% alpha, 38.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.68 Creating SS restraints... Processing helix chain 'A' and resid 63 through 67 removed outlier: 5.728A pdb=" N SER A 67 " --> pdb=" O ALA A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 77 No H-bonds generated for 'chain 'A' and resid 75 through 77' Processing helix chain 'A' and resid 88 through 92 Processing helix chain 'B' and resid 79 through 83 removed outlier: 3.758A pdb=" N PHE B 83 " --> pdb=" O PRO B 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 5 through 21 Proline residue: C 16 - end of helix Processing helix chain 'C' and resid 26 through 38 Processing helix chain 'C' and resid 97 through 113 Processing helix chain 'C' and resid 114 through 122 Processing helix chain 'C' and resid 125 through 140 removed outlier: 3.980A pdb=" N ALA C 140 " --> pdb=" O ARG C 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 149 through 151 No H-bonds generated for 'chain 'C' and resid 149 through 151' Processing helix chain 'H' and resid 53 through 57 Processing helix chain 'H' and resid 64 through 67 Processing helix chain 'H' and resid 89 through 93 Processing helix chain 'L' and resid 25 through 28 Processing helix chain 'L' and resid 77 through 81 removed outlier: 3.509A pdb=" N ASP L 81 " --> pdb=" O ALA L 78 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 7 Processing sheet with id=AA2, first strand: chain 'A' and resid 11 through 12 removed outlier: 6.709A pdb=" N VAL A 36 " --> pdb=" O HIS A 52 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N HIS A 52 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N TRP A 38 " --> pdb=" O LEU A 50 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N HIS A 52 " --> pdb=" O PHE A 60 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N PHE A 60 " --> pdb=" O HIS A 52 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 4 through 7 Processing sheet with id=AA4, first strand: chain 'B' and resid 11 through 13 removed outlier: 3.837A pdb=" N LEU B 11 " --> pdb=" O ASN B 103 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N GLU B 105 " --> pdb=" O LEU B 11 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ALA B 13 " --> pdb=" O GLU B 105 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N LEU B 33 " --> pdb=" O TYR B 49 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N TYR B 49 " --> pdb=" O LEU B 33 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N TRP B 35 " --> pdb=" O LEU B 47 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 41 through 42 removed outlier: 7.251A pdb=" N GLY C 48 " --> pdb=" O VAL C 89 " (cutoff:3.500A) removed outlier: 8.437A pdb=" N PHE C 91 " --> pdb=" O GLY C 48 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ALA C 50 " --> pdb=" O PHE C 91 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N LEU C 93 " --> pdb=" O ALA C 50 " (cutoff:3.500A) removed outlier: 9.742A pdb=" N LYS C 71 " --> pdb=" O PRO C 86 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N ARG C 88 " --> pdb=" O LEU C 69 " (cutoff:3.500A) removed outlier: 8.544A pdb=" N ARG C 154 " --> pdb=" O ILE C 64 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N VAL C 66 " --> pdb=" O ARG C 154 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N LEU C 156 " --> pdb=" O VAL C 66 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N ILE C 68 " --> pdb=" O LEU C 156 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA7, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.597A pdb=" N TRP H 33 " --> pdb=" O THR H 101 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 11 through 12 removed outlier: 7.044A pdb=" N CYS H 98 " --> pdb=" O TRP H 121 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N TRP H 121 " --> pdb=" O CYS H 98 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ARG H 100 " --> pdb=" O GLN H 119 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 3 through 5 Processing sheet with id=AB1, first strand: chain 'L' and resid 8 through 12 removed outlier: 6.296A pdb=" N GLN L 35 " --> pdb=" O LEU L 44 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N LEU L 44 " --> pdb=" O GLN L 35 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 8 through 12 213 hydrogen bonds defined for protein. 525 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: 1.35 Time building geometry restraints manager: 1.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.27: 788 1.27 - 1.41: 1288 1.41 - 1.55: 2767 1.55 - 1.69: 64 1.69 - 1.82: 26 Bond restraints: 4933 Sorted by residual: bond pdb=" CG PRO C 141 " pdb=" CD PRO C 141 " ideal model delta sigma weight residual 1.503 1.131 0.372 3.40e-02 8.65e+02 1.20e+02 bond pdb=" N PRO C 141 " pdb=" CD PRO C 141 " ideal model delta sigma weight residual 1.473 1.554 -0.081 1.40e-02 5.10e+03 3.36e+01 bond pdb=" CB PRO C 82 " pdb=" CG PRO C 82 " ideal model delta sigma weight residual 1.492 1.658 -0.166 5.00e-02 4.00e+02 1.10e+01 bond pdb=" CB PRO C 141 " pdb=" CG PRO C 141 " ideal model delta sigma weight residual 1.492 1.593 -0.101 5.00e-02 4.00e+02 4.08e+00 bond pdb=" CB MET C 124 " pdb=" CG MET C 124 " ideal model delta sigma weight residual 1.520 1.463 0.057 3.00e-02 1.11e+03 3.60e+00 ... (remaining 4928 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.46: 6451 3.46 - 6.92: 217 6.92 - 10.38: 16 10.38 - 13.84: 6 13.84 - 17.30: 3 Bond angle restraints: 6693 Sorted by residual: angle pdb=" CA PRO C 141 " pdb=" N PRO C 141 " pdb=" CD PRO C 141 " ideal model delta sigma weight residual 112.00 94.70 17.30 1.40e+00 5.10e-01 1.53e+02 angle pdb=" N PRO C 141 " pdb=" CD PRO C 141 " pdb=" CG PRO C 141 " ideal model delta sigma weight residual 103.20 86.58 16.62 1.50e+00 4.44e-01 1.23e+02 angle pdb=" CA PRO C 82 " pdb=" N PRO C 82 " pdb=" CD PRO C 82 " ideal model delta sigma weight residual 112.00 99.04 12.96 1.40e+00 5.10e-01 8.57e+01 angle pdb=" CA PRO C 141 " pdb=" CB PRO C 141 " pdb=" CG PRO C 141 " ideal model delta sigma weight residual 104.50 90.52 13.98 1.90e+00 2.77e-01 5.41e+01 angle pdb=" CA TYR L 47 " pdb=" CB TYR L 47 " pdb=" CG TYR L 47 " ideal model delta sigma weight residual 113.90 122.48 -8.58 1.80e+00 3.09e-01 2.27e+01 ... (remaining 6688 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 2625 17.91 - 35.81: 217 35.81 - 53.72: 61 53.72 - 71.62: 10 71.62 - 89.53: 3 Dihedral angle restraints: 2916 sinusoidal: 1176 harmonic: 1740 Sorted by residual: dihedral pdb=" CA PHE H 29 " pdb=" C PHE H 29 " pdb=" N ASP H 30 " pdb=" CA ASP H 30 " ideal model delta harmonic sigma weight residual 180.00 -161.42 -18.58 0 5.00e+00 4.00e-02 1.38e+01 dihedral pdb=" CB GLU L 6 " pdb=" CG GLU L 6 " pdb=" CD GLU L 6 " pdb=" OE1 GLU L 6 " ideal model delta sinusoidal sigma weight residual 0.00 89.53 -89.53 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CA ASN H 79 " pdb=" CB ASN H 79 " pdb=" CG ASN H 79 " pdb=" OD1 ASN H 79 " ideal model delta sinusoidal sigma weight residual 120.00 -172.97 -67.03 2 2.00e+01 2.50e-03 1.02e+01 ... (remaining 2913 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 532 0.069 - 0.138: 161 0.138 - 0.207: 28 0.207 - 0.275: 2 0.275 - 0.344: 2 Chirality restraints: 725 Sorted by residual: chirality pdb=" CA PRO C 82 " pdb=" N PRO C 82 " pdb=" C PRO C 82 " pdb=" CB PRO C 82 " both_signs ideal model delta sigma weight residual False 2.72 2.37 0.34 2.00e-01 2.50e+01 2.96e+00 chirality pdb=" CA PRO C 141 " pdb=" N PRO C 141 " pdb=" C PRO C 141 " pdb=" CB PRO C 141 " both_signs ideal model delta sigma weight residual False 2.72 2.38 0.34 2.00e-01 2.50e+01 2.90e+00 chirality pdb=" CB ILE A 71 " pdb=" CA ILE A 71 " pdb=" CG1 ILE A 71 " pdb=" CG2 ILE A 71 " both_signs ideal model delta sigma weight residual False 2.64 2.90 -0.26 2.00e-01 2.50e+01 1.69e+00 ... (remaining 722 not shown) Planarity restraints: 858 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 35 " 0.042 2.00e-02 2.50e+03 3.03e-02 2.30e+01 pdb=" CG TRP B 35 " -0.083 2.00e-02 2.50e+03 pdb=" CD1 TRP B 35 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 TRP B 35 " 0.005 2.00e-02 2.50e+03 pdb=" NE1 TRP B 35 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP B 35 " 0.006 2.00e-02 2.50e+03 pdb=" CE3 TRP B 35 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 35 " 0.005 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 35 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP B 35 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR H 111 " -0.081 5.00e-02 4.00e+02 1.20e-01 2.29e+01 pdb=" N PRO H 112 " 0.207 5.00e-02 4.00e+02 pdb=" CA PRO H 112 " -0.062 5.00e-02 4.00e+02 pdb=" CD PRO H 112 " -0.064 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA C 140 " 0.087 5.00e-02 4.00e+02 1.17e-01 2.20e+01 pdb=" N PRO C 141 " -0.202 5.00e-02 4.00e+02 pdb=" CA PRO C 141 " 0.052 5.00e-02 4.00e+02 pdb=" CD PRO C 141 " 0.063 5.00e-02 4.00e+02 ... (remaining 855 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.70: 156 2.70 - 3.25: 4474 3.25 - 3.80: 7562 3.80 - 4.35: 9516 4.35 - 4.90: 15908 Nonbonded interactions: 37616 Sorted by model distance: nonbonded pdb=" O GLY L 75 " pdb=" NE2 GLN L 77 " model vdw 2.144 3.120 nonbonded pdb=" OD1 ASP A 91 " pdb=" OH TYR A 95 " model vdw 2.157 3.040 nonbonded pdb=" NE2 GLN A 13 " pdb=" O PRO A 14 " model vdw 2.201 3.120 nonbonded pdb=" NE2 GLN A 13 " pdb=" OE1 GLN A 16 " model vdw 2.245 3.120 nonbonded pdb=" OH TYR A 104 " pdb=" NH1 ARG C 131 " model vdw 2.264 3.120 ... (remaining 37611 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 3.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 16.960 Find NCS groups from input model: 0.060 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: 23.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 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 : 0.010 0.372 4933 Z= 0.616 Angle : 1.446 17.297 6693 Z= 0.795 Chirality : 0.066 0.344 725 Planarity : 0.011 0.120 857 Dihedral : 14.594 89.530 1802 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 0.00 % Allowed : 23.26 % Favored : 76.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.33), residues: 604 helix: 0.20 (0.53), residues: 75 sheet: 1.06 (0.34), residues: 212 loop : 0.54 (0.35), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.083 0.005 TRP B 35 HIS 0.016 0.003 HIS L 29 PHE 0.063 0.007 PHE H 107 TYR 0.064 0.006 TYR L 85 ARG 0.018 0.002 ARG C 131 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 154 time to evaluate : 0.569 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 87 TYR cc_start: 0.8514 (m-80) cc_final: 0.8310 (m-80) REVERT: C 29 GLU cc_start: 0.8116 (mp0) cc_final: 0.7851 (mp0) REVERT: H 47 TRP cc_start: 0.8838 (t60) cc_final: 0.8534 (t60) REVERT: H 61 ASP cc_start: 0.7857 (m-30) cc_final: 0.7630 (m-30) REVERT: L 60 PHE cc_start: 0.6118 (p90) cc_final: 0.5839 (p90) outliers start: 0 outliers final: 0 residues processed: 154 average time/residue: 0.2051 time to fit residues: 38.8655 Evaluate side-chains 119 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 48 optimal weight: 10.0000 chunk 43 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 29 optimal weight: 0.6980 chunk 23 optimal weight: 0.5980 chunk 45 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 52 optimal weight: 0.5980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 GLN A 16 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.1816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 4933 Z= 0.292 Angle : 0.766 11.645 6693 Z= 0.391 Chirality : 0.047 0.198 725 Planarity : 0.005 0.063 857 Dihedral : 5.283 34.174 712 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 3.88 % Allowed : 19.96 % Favored : 76.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.33), residues: 604 helix: 1.03 (0.60), residues: 77 sheet: 1.23 (0.33), residues: 221 loop : 0.13 (0.35), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.003 TRP B 35 HIS 0.006 0.001 HIS L 29 PHE 0.016 0.002 PHE H 107 TYR 0.017 0.002 TYR L 85 ARG 0.006 0.001 ARG C 131 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 129 time to evaluate : 0.647 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 GLN cc_start: 0.8007 (tm-30) cc_final: 0.7698 (tm-30) REVERT: A 16 GLN cc_start: 0.7940 (mm-40) cc_final: 0.7141 (mm-40) REVERT: A 102 GLU cc_start: 0.8564 (tm-30) cc_final: 0.8202 (tm-30) REVERT: B 61 ARG cc_start: 0.7872 (ptt180) cc_final: 0.7636 (ptt180) REVERT: B 83 PHE cc_start: 0.7602 (m-80) cc_final: 0.7399 (m-80) REVERT: B 87 TYR cc_start: 0.8392 (m-80) cc_final: 0.8163 (m-80) REVERT: L 60 PHE cc_start: 0.6586 (p90) cc_final: 0.6360 (p90) outliers start: 20 outliers final: 10 residues processed: 142 average time/residue: 0.1761 time to fit residues: 31.6130 Evaluate side-chains 117 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 107 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain C residue 58 TYR Chi-restraints excluded: chain C residue 76 SER Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 98 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 29 optimal weight: 2.9990 chunk 16 optimal weight: 0.3980 chunk 43 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 57 optimal weight: 0.7980 chunk 46 optimal weight: 0.8980 chunk 17 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.2557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 4933 Z= 0.307 Angle : 0.740 11.057 6693 Z= 0.374 Chirality : 0.045 0.182 725 Planarity : 0.005 0.064 857 Dihedral : 5.130 31.452 712 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 12.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 4.26 % Allowed : 20.74 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.33), residues: 604 helix: 0.61 (0.58), residues: 77 sheet: 1.28 (0.33), residues: 220 loop : 0.05 (0.36), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP B 35 HIS 0.006 0.002 HIS L 29 PHE 0.020 0.002 PHE C 91 TYR 0.018 0.002 TYR L 85 ARG 0.006 0.001 ARG C 37 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 119 time to evaluate : 0.522 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 ASP cc_start: 0.8578 (p0) cc_final: 0.7890 (p0) REVERT: A 102 GLU cc_start: 0.8563 (tm-30) cc_final: 0.8251 (tm-30) REVERT: B 36 TYR cc_start: 0.7996 (m-80) cc_final: 0.7003 (m-10) REVERT: B 61 ARG cc_start: 0.7856 (ptt180) cc_final: 0.7641 (ptt180) REVERT: B 83 PHE cc_start: 0.7720 (m-80) cc_final: 0.7428 (m-80) REVERT: B 87 TYR cc_start: 0.8459 (m-80) cc_final: 0.8235 (m-80) REVERT: L 60 PHE cc_start: 0.6947 (p90) cc_final: 0.6716 (p90) outliers start: 22 outliers final: 14 residues processed: 129 average time/residue: 0.1539 time to fit residues: 25.7430 Evaluate side-chains 122 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 108 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 PHE Chi-restraints excluded: chain A residue 66 LYS Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 58 TYR Chi-restraints excluded: chain C residue 76 SER Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain L residue 97 SER Chi-restraints excluded: chain L residue 98 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 27 optimal weight: 2.9990 chunk 5 optimal weight: 0.5980 chunk 25 optimal weight: 0.9990 chunk 35 optimal weight: 0.9990 chunk 52 optimal weight: 0.0970 chunk 56 optimal weight: 0.1980 chunk 50 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 46 optimal weight: 2.9990 chunk 31 optimal weight: 0.6980 chunk 0 optimal weight: 6.9990 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.2773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 4933 Z= 0.199 Angle : 0.691 10.600 6693 Z= 0.341 Chirality : 0.044 0.178 725 Planarity : 0.004 0.038 857 Dihedral : 4.873 30.096 712 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 2.71 % Allowed : 21.71 % Favored : 75.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.33), residues: 604 helix: 0.72 (0.58), residues: 77 sheet: 1.15 (0.32), residues: 223 loop : 0.03 (0.36), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 35 HIS 0.005 0.001 HIS L 29 PHE 0.015 0.002 PHE A 81 TYR 0.018 0.001 TYR L 85 ARG 0.003 0.001 ARG L 22 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 121 time to evaluate : 0.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 ASP cc_start: 0.8537 (p0) cc_final: 0.7711 (p0) REVERT: A 102 GLU cc_start: 0.8559 (tm-30) cc_final: 0.8271 (tm-30) REVERT: B 36 TYR cc_start: 0.8094 (m-80) cc_final: 0.7883 (m-10) REVERT: B 83 PHE cc_start: 0.7741 (m-80) cc_final: 0.7375 (m-80) outliers start: 14 outliers final: 10 residues processed: 126 average time/residue: 0.1568 time to fit residues: 25.3507 Evaluate side-chains 114 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 104 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 58 TYR Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain L residue 97 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 41 optimal weight: 3.9990 chunk 23 optimal weight: 0.5980 chunk 47 optimal weight: 0.1980 chunk 38 optimal weight: 0.9980 chunk 0 optimal weight: 6.9990 chunk 28 optimal weight: 5.9990 chunk 50 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 chunk 18 optimal weight: 0.9990 chunk 11 optimal weight: 4.9990 chunk 32 optimal weight: 0.6980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 76 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.3106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 4933 Z= 0.232 Angle : 0.683 10.602 6693 Z= 0.339 Chirality : 0.043 0.173 725 Planarity : 0.004 0.035 857 Dihedral : 4.807 28.758 712 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 3.10 % Allowed : 22.67 % Favored : 74.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.33), residues: 604 helix: 0.80 (0.60), residues: 77 sheet: 1.25 (0.33), residues: 219 loop : -0.05 (0.36), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP B 35 HIS 0.004 0.001 HIS L 29 PHE 0.013 0.002 PHE H 107 TYR 0.018 0.001 TYR L 85 ARG 0.006 0.001 ARG B 61 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 109 time to evaluate : 0.568 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 13 GLN cc_start: 0.7851 (tm-30) cc_final: 0.7269 (tm-30) REVERT: A 56 ASP cc_start: 0.8530 (p0) cc_final: 0.7641 (p0) REVERT: A 102 GLU cc_start: 0.8521 (tm-30) cc_final: 0.8231 (tm-30) REVERT: B 36 TYR cc_start: 0.8273 (m-80) cc_final: 0.8012 (m-10) REVERT: B 83 PHE cc_start: 0.7836 (m-80) cc_final: 0.7226 (m-80) outliers start: 16 outliers final: 11 residues processed: 119 average time/residue: 0.1640 time to fit residues: 25.1739 Evaluate side-chains 114 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 103 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain C residue 58 TYR Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 117 TYR Chi-restraints excluded: chain L residue 97 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 13 optimal weight: 3.9990 chunk 56 optimal weight: 4.9990 chunk 46 optimal weight: 3.9990 chunk 25 optimal weight: 0.9980 chunk 4 optimal weight: 0.7980 chunk 18 optimal weight: 0.7980 chunk 29 optimal weight: 0.0770 chunk 54 optimal weight: 6.9990 chunk 6 optimal weight: 0.9980 chunk 31 optimal weight: 0.5980 chunk 40 optimal weight: 0.6980 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 35 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.3335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4933 Z= 0.213 Angle : 0.677 10.395 6693 Z= 0.336 Chirality : 0.044 0.164 725 Planarity : 0.004 0.034 857 Dihedral : 4.747 27.378 712 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.91 % Allowed : 22.67 % Favored : 74.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.34), residues: 604 helix: 0.85 (0.61), residues: 77 sheet: 1.27 (0.33), residues: 219 loop : 0.00 (0.36), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 35 HIS 0.004 0.001 HIS L 29 PHE 0.016 0.002 PHE B 83 TYR 0.020 0.001 TYR L 85 ARG 0.002 0.000 ARG L 22 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 111 time to evaluate : 0.593 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 56 ASP cc_start: 0.8483 (p0) cc_final: 0.7582 (p0) REVERT: B 36 TYR cc_start: 0.8295 (m-80) cc_final: 0.7939 (m-10) REVERT: B 87 TYR cc_start: 0.8219 (m-80) cc_final: 0.7852 (m-80) outliers start: 15 outliers final: 11 residues processed: 118 average time/residue: 0.1714 time to fit residues: 25.8517 Evaluate side-chains 113 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 102 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain C residue 58 TYR Chi-restraints excluded: chain C residue 76 SER Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain L residue 35 GLN Chi-restraints excluded: chain L residue 36 LYS Chi-restraints excluded: chain L residue 97 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 31 optimal weight: 0.9990 chunk 47 optimal weight: 0.8980 chunk 55 optimal weight: 0.9990 chunk 34 optimal weight: 0.9980 chunk 25 optimal weight: 0.3980 chunk 22 optimal weight: 0.2980 chunk 33 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 10 optimal weight: 0.6980 chunk 35 optimal weight: 0.7980 chunk 38 optimal weight: 0.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 GLN L 35 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.3467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4933 Z= 0.217 Angle : 0.682 11.528 6693 Z= 0.335 Chirality : 0.043 0.164 725 Planarity : 0.004 0.033 857 Dihedral : 4.755 27.733 712 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 13.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 3.88 % Allowed : 24.22 % Favored : 71.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.34), residues: 604 helix: 0.78 (0.60), residues: 77 sheet: 1.15 (0.32), residues: 223 loop : 0.02 (0.37), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 35 HIS 0.004 0.001 HIS L 29 PHE 0.012 0.002 PHE H 107 TYR 0.019 0.001 TYR L 85 ARG 0.006 0.000 ARG H 100 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 109 time to evaluate : 0.508 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 56 ASP cc_start: 0.8495 (p0) cc_final: 0.7549 (p0) REVERT: B 36 TYR cc_start: 0.8305 (m-80) cc_final: 0.7907 (m-10) REVERT: B 87 TYR cc_start: 0.8230 (m-80) cc_final: 0.7843 (m-80) REVERT: C 22 MET cc_start: 0.8379 (mmp) cc_final: 0.8038 (mmp) REVERT: C 124 MET cc_start: 0.8659 (mtt) cc_final: 0.8407 (mtt) outliers start: 20 outliers final: 18 residues processed: 121 average time/residue: 0.1544 time to fit residues: 24.2636 Evaluate side-chains 122 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 104 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 LYS Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain C residue 58 TYR Chi-restraints excluded: chain C residue 76 SER Chi-restraints excluded: chain C residue 80 GLN Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 117 TYR Chi-restraints excluded: chain L residue 35 GLN Chi-restraints excluded: chain L residue 86 CYS Chi-restraints excluded: chain L residue 97 SER Chi-restraints excluded: chain L residue 108 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 27 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 43 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 53 optimal weight: 0.4980 chunk 48 optimal weight: 6.9990 chunk 52 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 chunk 22 optimal weight: 0.1980 chunk 40 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 155 HIS L 35 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.3576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4933 Z= 0.213 Angle : 0.693 11.433 6693 Z= 0.341 Chirality : 0.043 0.163 725 Planarity : 0.004 0.037 857 Dihedral : 4.701 26.944 712 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 13.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 3.88 % Allowed : 24.81 % Favored : 71.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.34), residues: 604 helix: 0.75 (0.60), residues: 77 sheet: 1.17 (0.33), residues: 217 loop : -0.09 (0.36), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 35 HIS 0.004 0.001 HIS L 29 PHE 0.012 0.002 PHE A 105 TYR 0.020 0.001 TYR L 85 ARG 0.007 0.000 ARG H 100 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 111 time to evaluate : 0.566 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 56 ASP cc_start: 0.8482 (p0) cc_final: 0.7528 (p0) REVERT: B 36 TYR cc_start: 0.8349 (m-80) cc_final: 0.7884 (m-10) REVERT: B 87 TYR cc_start: 0.8239 (m-80) cc_final: 0.7841 (m-80) REVERT: C 22 MET cc_start: 0.8390 (mmp) cc_final: 0.8082 (mmp) REVERT: C 124 MET cc_start: 0.8614 (mtt) cc_final: 0.8396 (mtt) outliers start: 20 outliers final: 19 residues processed: 122 average time/residue: 0.1603 time to fit residues: 25.2577 Evaluate side-chains 124 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 105 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 LYS Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain C residue 58 TYR Chi-restraints excluded: chain C residue 76 SER Chi-restraints excluded: chain C residue 80 GLN Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 117 TYR Chi-restraints excluded: chain L residue 35 GLN Chi-restraints excluded: chain L residue 44 LEU Chi-restraints excluded: chain L residue 86 CYS Chi-restraints excluded: chain L residue 97 SER Chi-restraints excluded: chain L residue 108 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 47 optimal weight: 0.0070 chunk 49 optimal weight: 10.0000 chunk 51 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 55 optimal weight: 4.9990 chunk 33 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 chunk 53 optimal weight: 0.1980 chunk 46 optimal weight: 0.6980 overall best weight: 0.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.3703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4933 Z= 0.217 Angle : 0.696 10.322 6693 Z= 0.344 Chirality : 0.043 0.164 725 Planarity : 0.004 0.033 857 Dihedral : 4.729 26.201 712 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 13.38 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.15 % Favored : 96.69 % Rotamer: Outliers : 3.68 % Allowed : 25.39 % Favored : 70.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.34), residues: 604 helix: 0.76 (0.60), residues: 77 sheet: 1.17 (0.33), residues: 217 loop : -0.11 (0.36), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 35 HIS 0.004 0.001 HIS L 29 PHE 0.019 0.002 PHE A 81 TYR 0.018 0.001 TYR L 85 ARG 0.006 0.000 ARG H 100 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 111 time to evaluate : 0.506 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 56 ASP cc_start: 0.8477 (p0) cc_final: 0.7510 (p0) REVERT: B 36 TYR cc_start: 0.8359 (m-80) cc_final: 0.7870 (m-10) REVERT: C 22 MET cc_start: 0.8391 (mmp) cc_final: 0.8120 (mmp) REVERT: C 124 MET cc_start: 0.8613 (mtt) cc_final: 0.8405 (mtt) outliers start: 19 outliers final: 18 residues processed: 122 average time/residue: 0.1470 time to fit residues: 23.4705 Evaluate side-chains 124 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 106 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain C residue 58 TYR Chi-restraints excluded: chain C residue 76 SER Chi-restraints excluded: chain C residue 80 GLN Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 117 TYR Chi-restraints excluded: chain L residue 35 GLN Chi-restraints excluded: chain L residue 44 LEU Chi-restraints excluded: chain L residue 86 CYS Chi-restraints excluded: chain L residue 97 SER Chi-restraints excluded: chain L residue 108 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 4 optimal weight: 0.8980 chunk 35 optimal weight: 0.9980 chunk 28 optimal weight: 4.9990 chunk 36 optimal weight: 9.9990 chunk 49 optimal weight: 10.0000 chunk 14 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 chunk 46 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.3874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 4933 Z= 0.292 Angle : 0.730 10.371 6693 Z= 0.365 Chirality : 0.045 0.170 725 Planarity : 0.004 0.032 857 Dihedral : 4.973 25.375 712 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 15.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 3.88 % Allowed : 25.78 % Favored : 70.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.33), residues: 604 helix: 0.54 (0.60), residues: 77 sheet: 1.07 (0.33), residues: 219 loop : -0.18 (0.36), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 35 HIS 0.004 0.001 HIS B 30 PHE 0.016 0.002 PHE C 117 TYR 0.020 0.002 TYR B 36 ARG 0.005 0.000 ARG H 100 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 110 time to evaluate : 0.572 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 LYS cc_start: 0.7203 (OUTLIER) cc_final: 0.6764 (tppt) REVERT: A 104 TYR cc_start: 0.8365 (m-80) cc_final: 0.7979 (m-80) REVERT: B 36 TYR cc_start: 0.7804 (m-80) cc_final: 0.7536 (m-80) REVERT: C 22 MET cc_start: 0.8402 (mmp) cc_final: 0.8133 (mmp) REVERT: C 124 MET cc_start: 0.8634 (mtt) cc_final: 0.8423 (mtt) outliers start: 20 outliers final: 17 residues processed: 123 average time/residue: 0.1556 time to fit residues: 25.1522 Evaluate side-chains 121 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 103 time to evaluate : 1.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 LYS Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain C residue 58 TYR Chi-restraints excluded: chain C residue 76 SER Chi-restraints excluded: chain C residue 80 GLN Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 117 TYR Chi-restraints excluded: chain L residue 86 CYS Chi-restraints excluded: chain L residue 97 SER Chi-restraints excluded: chain L residue 108 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 47 optimal weight: 0.0980 chunk 5 optimal weight: 0.6980 chunk 8 optimal weight: 0.9990 chunk 40 optimal weight: 0.9990 chunk 2 optimal weight: 0.8980 chunk 33 optimal weight: 0.9990 chunk 52 optimal weight: 0.9990 chunk 30 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 36 optimal weight: 9.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.106131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.086187 restraints weight = 10480.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.089402 restraints weight = 6601.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.091757 restraints weight = 4713.968| |-----------------------------------------------------------------------------| r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.4051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 4933 Z= 0.243 Angle : 0.729 10.189 6693 Z= 0.361 Chirality : 0.044 0.165 725 Planarity : 0.004 0.032 857 Dihedral : 4.921 24.993 712 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 14.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 3.49 % Allowed : 26.16 % Favored : 70.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.33), residues: 604 helix: 0.63 (0.59), residues: 77 sheet: 1.04 (0.33), residues: 217 loop : -0.26 (0.35), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 35 HIS 0.004 0.001 HIS L 29 PHE 0.019 0.002 PHE A 81 TYR 0.036 0.002 TYR B 87 ARG 0.005 0.000 ARG H 100 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1539.34 seconds wall clock time: 28 minutes 52.33 seconds (1732.33 seconds total)