Starting phenix.real_space_refine on Wed Jan 17 20:54:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e2j_27838/01_2024/8e2j_27838_trim.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e2j_27838/01_2024/8e2j_27838.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.44 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e2j_27838/01_2024/8e2j_27838.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e2j_27838/01_2024/8e2j_27838.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e2j_27838/01_2024/8e2j_27838_trim.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e2j_27838/01_2024/8e2j_27838_trim.pdb" } resolution = 3.44 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= 0.031 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 10 5.16 5 C 2040 2.51 5 N 576 2.21 5 O 692 1.98 5 H 2694 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 6012 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 2721 Classifications: {'peptide': 173} Link IDs: {'TRANS': 172} Chain: "B" Number of atoms: 2721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 2721 Classifications: {'peptide': 173} Link IDs: {'TRANS': 172} Chain: "C" Number of atoms: 285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 285 Classifications: {'peptide': 57} Incomplete info: {'truncation_to_alanine': 57} Link IDs: {'TRANS': 56} Unresolved non-hydrogen bonds: 114 Unresolved non-hydrogen angles: 171 Unresolved non-hydrogen dihedrals: 57 Planarities with less than four sites: {'UNK:plan-1': 57} Unresolved non-hydrogen planarities: 57 Chain: "D" Number of atoms: 285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 285 Classifications: {'peptide': 57} Incomplete info: {'truncation_to_alanine': 57} Link IDs: {'TRANS': 56} Unresolved non-hydrogen bonds: 114 Unresolved non-hydrogen angles: 171 Unresolved non-hydrogen dihedrals: 57 Planarities with less than four sites: {'UNK:plan-1': 57} Unresolved non-hydrogen planarities: 57 Time building chain proxies: 3.33, per 1000 atoms: 0.55 Number of scatterers: 6012 At special positions: 0 Unit cell: (121.149, 121.149, 77.9675, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 10 16.00 O 692 8.00 N 576 7.00 C 2040 6.00 H 2694 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.40 Conformation dependent library (CDL) restraints added in 630.8 milliseconds 684 Ramachandran restraints generated. 342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 900 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 0 sheets defined 127.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'A' and resid 12 through 65 Processing helix chain 'A' and resid 73 through 120 Processing helix chain 'A' and resid 121 through 180 Processing helix chain 'B' and resid 13 through 65 Processing helix chain 'B' and resid 66 through 69 removed outlier: 4.560A pdb=" N MET B 69 " --> pdb=" O LEU B 66 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 66 through 69' Processing helix chain 'B' and resid 70 through 119 removed outlier: 5.045A pdb=" N GLU B 76 " --> pdb=" O GLU B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 180 Processing helix chain 'C' and resid 52 through 107 Processing helix chain 'D' and resid 52 through 107 removed outlier: 3.544A pdb=" N UNK D 57 " --> pdb=" O UNK D 53 " (cutoff:3.500A) 403 hydrogen bonds defined for protein. 1209 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: 2.35 Time building geometry restraints manager: 4.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 2694 1.03 - 1.22: 0 1.22 - 1.42: 1358 1.42 - 1.61: 1968 1.61 - 1.81: 20 Bond restraints: 6040 Sorted by residual: bond pdb=" CB THR B 27 " pdb=" CG2 THR B 27 " ideal model delta sigma weight residual 1.521 1.488 0.033 3.30e-02 9.18e+02 9.90e-01 bond pdb=" C LEU A 98 " pdb=" O LEU A 98 " ideal model delta sigma weight residual 1.237 1.225 0.011 1.17e-02 7.31e+03 9.50e-01 bond pdb=" C GLU B 140 " pdb=" O GLU B 140 " ideal model delta sigma weight residual 1.236 1.224 0.012 1.29e-02 6.01e+03 8.13e-01 bond pdb=" CB VAL B 26 " pdb=" CG2 VAL B 26 " ideal model delta sigma weight residual 1.521 1.492 0.029 3.30e-02 9.18e+02 7.88e-01 bond pdb=" C VAL B 26 " pdb=" N THR B 27 " ideal model delta sigma weight residual 1.335 1.323 0.012 1.36e-02 5.41e+03 7.80e-01 ... (remaining 6035 not shown) Histogram of bond angle deviations from ideal: 99.92 - 106.72: 28 106.72 - 113.52: 6898 113.52 - 120.32: 1857 120.32 - 127.13: 1850 127.13 - 133.93: 15 Bond angle restraints: 10648 Sorted by residual: angle pdb=" CA TYR A 95 " pdb=" CB TYR A 95 " pdb=" CG TYR A 95 " ideal model delta sigma weight residual 113.90 119.63 -5.73 1.80e+00 3.09e-01 1.01e+01 angle pdb=" C UNK C 91 " pdb=" N UNK C 92 " pdb=" CA UNK C 92 " ideal model delta sigma weight residual 121.70 125.93 -4.23 1.80e+00 3.09e-01 5.53e+00 angle pdb=" N GLU A 183 " pdb=" CA GLU A 183 " pdb=" C GLU A 183 " ideal model delta sigma weight residual 110.80 115.19 -4.39 2.13e+00 2.20e-01 4.24e+00 angle pdb=" C HIS A 131 " pdb=" N ILE A 132 " pdb=" CA ILE A 132 " ideal model delta sigma weight residual 120.60 122.99 -2.39 1.29e+00 6.01e-01 3.43e+00 angle pdb=" C ALA B 44 " pdb=" N ILE B 45 " pdb=" CA ILE B 45 " ideal model delta sigma weight residual 120.53 123.05 -2.52 1.41e+00 5.03e-01 3.18e+00 ... (remaining 10643 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.77: 2672 17.77 - 35.54: 148 35.54 - 53.31: 34 53.31 - 71.08: 9 71.08 - 88.85: 9 Dihedral angle restraints: 2872 sinusoidal: 1384 harmonic: 1488 Sorted by residual: dihedral pdb=" CA GLU A 72 " pdb=" C GLU A 72 " pdb=" N GLU A 73 " pdb=" CA GLU A 73 " ideal model delta harmonic sigma weight residual 180.00 162.32 17.68 0 5.00e+00 4.00e-02 1.25e+01 dihedral pdb=" CA LEU A 66 " pdb=" C LEU A 66 " pdb=" N GLY A 67 " pdb=" CA GLY A 67 " ideal model delta harmonic sigma weight residual -180.00 -162.76 -17.24 0 5.00e+00 4.00e-02 1.19e+01 dihedral pdb=" CA UNK C 51 " pdb=" C UNK C 51 " pdb=" N UNK C 52 " pdb=" CA UNK C 52 " ideal model delta harmonic sigma weight residual -180.00 -163.77 -16.23 0 5.00e+00 4.00e-02 1.05e+01 ... (remaining 2869 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 420 0.030 - 0.061: 119 0.061 - 0.091: 12 0.091 - 0.121: 2 0.121 - 0.151: 1 Chirality restraints: 554 Sorted by residual: chirality pdb=" CA TYR A 95 " pdb=" N TYR A 95 " pdb=" C TYR A 95 " pdb=" CB TYR A 95 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.73e-01 chirality pdb=" CA ILE A 132 " pdb=" N ILE A 132 " pdb=" C ILE A 132 " pdb=" CB ILE A 132 " both_signs ideal model delta sigma weight residual False 2.43 2.53 -0.10 2.00e-01 2.50e+01 2.51e-01 chirality pdb=" CA GLU A 183 " pdb=" N GLU A 183 " pdb=" C GLU A 183 " pdb=" CB GLU A 183 " both_signs ideal model delta sigma weight residual False 2.51 2.42 0.09 2.00e-01 2.50e+01 2.19e-01 ... (remaining 551 not shown) Planarity restraints: 936 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 78 " 0.013 2.00e-02 2.50e+03 1.83e-02 1.34e+01 pdb=" CG TRP B 78 " -0.016 2.00e-02 2.50e+03 pdb=" CD1 TRP B 78 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 TRP B 78 " -0.006 2.00e-02 2.50e+03 pdb=" NE1 TRP B 78 " -0.021 2.00e-02 2.50e+03 pdb=" CE2 TRP B 78 " 0.013 2.00e-02 2.50e+03 pdb=" CE3 TRP B 78 " -0.029 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 78 " 0.020 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 78 " 0.010 2.00e-02 2.50e+03 pdb=" CH2 TRP B 78 " 0.034 2.00e-02 2.50e+03 pdb=" HD1 TRP B 78 " -0.001 2.00e-02 2.50e+03 pdb=" HE1 TRP B 78 " 0.018 2.00e-02 2.50e+03 pdb=" HE3 TRP B 78 " -0.000 2.00e-02 2.50e+03 pdb=" HZ2 TRP B 78 " -0.019 2.00e-02 2.50e+03 pdb=" HZ3 TRP B 78 " 0.012 2.00e-02 2.50e+03 pdb=" HH2 TRP B 78 " -0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 165 " -0.018 2.00e-02 2.50e+03 3.53e-02 1.25e+01 pdb=" C THR B 165 " 0.061 2.00e-02 2.50e+03 pdb=" O THR B 165 " -0.023 2.00e-02 2.50e+03 pdb=" N GLN B 166 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 59 " -0.007 2.00e-02 2.50e+03 2.02e-02 1.22e+01 pdb=" CG TYR B 59 " 0.013 2.00e-02 2.50e+03 pdb=" CD1 TYR B 59 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 TYR B 59 " 0.010 2.00e-02 2.50e+03 pdb=" CE1 TYR B 59 " 0.041 2.00e-02 2.50e+03 pdb=" CE2 TYR B 59 " 0.016 2.00e-02 2.50e+03 pdb=" CZ TYR B 59 " 0.028 2.00e-02 2.50e+03 pdb=" OH TYR B 59 " -0.027 2.00e-02 2.50e+03 pdb=" HD1 TYR B 59 " -0.020 2.00e-02 2.50e+03 pdb=" HD2 TYR B 59 " -0.010 2.00e-02 2.50e+03 pdb=" HE1 TYR B 59 " -0.014 2.00e-02 2.50e+03 pdb=" HE2 TYR B 59 " -0.020 2.00e-02 2.50e+03 ... (remaining 933 not shown) Histogram of nonbonded interaction distances: 1.46 - 2.09: 140 2.09 - 2.72: 9530 2.72 - 3.34: 17591 3.34 - 3.97: 20508 3.97 - 4.60: 33116 Nonbonded interactions: 80885 Sorted by model distance: nonbonded pdb=" O ARG A 21 " pdb=" HG SER A 24 " model vdw 1.462 1.850 nonbonded pdb=" O GLN B 61 " pdb=" HG SER B 64 " model vdw 1.559 1.850 nonbonded pdb=" O ARG B 21 " pdb=" HG SER B 24 " model vdw 1.606 1.850 nonbonded pdb="HH11 ARG B 129 " pdb=" OD1 ASN B 130 " model vdw 1.611 1.850 nonbonded pdb=" O GLN A 61 " pdb=" HG SER A 64 " model vdw 1.611 1.850 ... (remaining 80880 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' } ncs_group { reference = chain 'C' selection = chain 'D' } 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: 1.770 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: 0.110 Extract box with map and model: 8.940 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 23.770 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.070 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:3.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7060 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 0.033 3346 Z= 0.207 Angle : 0.629 5.734 4544 Z= 0.386 Chirality : 0.028 0.151 554 Planarity : 0.008 0.084 592 Dihedral : 15.861 88.851 1154 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.70 % Allowed : 6.08 % Favored : 91.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.37), residues: 342 helix: 0.02 (0.24), residues: 315 sheet: None (None), residues: 0 loop : -1.70 (1.15), residues: 27 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.010 TRP B 78 HIS 0.010 0.003 HIS A 131 PHE 0.017 0.009 PHE B 33 TYR 0.043 0.007 TYR A 95 ARG 0.018 0.002 ARG A 147 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 684 Ramachandran restraints generated. 342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 684 Ramachandran restraints generated. 342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 120 time to evaluate : 0.435 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 MET cc_start: 0.8291 (ttp) cc_final: 0.8078 (tmm) REVERT: A 145 LEU cc_start: 0.8834 (mp) cc_final: 0.8594 (tp) REVERT: B 33 PHE cc_start: 0.8349 (t80) cc_final: 0.8108 (t80) outliers start: 8 outliers final: 5 residues processed: 124 average time/residue: 0.5077 time to fit residues: 70.0684 Evaluate side-chains 97 residues out of total 296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 92 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 TYR Chi-restraints excluded: chain A residue 111 MET Chi-restraints excluded: chain A residue 147 ARG Chi-restraints excluded: chain B residue 95 TYR Chi-restraints excluded: chain B residue 98 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 37 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 22 optimal weight: 4.9990 chunk 17 optimal weight: 4.9990 chunk 34 optimal weight: 20.0000 chunk 13 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 39 optimal weight: 30.0000 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 157 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7233 moved from start: 0.4023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 3346 Z= 0.337 Angle : 0.590 5.000 4544 Z= 0.343 Chirality : 0.027 0.111 554 Planarity : 0.004 0.035 592 Dihedral : 6.429 55.579 503 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Rotamer: Outliers : 3.72 % Allowed : 12.50 % Favored : 83.78 % 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: 1.91 (0.42), residues: 342 helix: 1.47 (0.26), residues: 320 sheet: None (None), residues: 0 loop : -1.20 (1.56), residues: 22 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 78 HIS 0.005 0.002 HIS A 131 PHE 0.017 0.005 PHE A 33 TYR 0.024 0.002 TYR A 95 ARG 0.005 0.001 ARG B 20 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 684 Ramachandran restraints generated. 342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 684 Ramachandran restraints generated. 342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 89 time to evaluate : 0.471 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 10 residues processed: 95 average time/residue: 0.4461 time to fit residues: 48.2509 Evaluate side-chains 93 residues out of total 296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 83 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 95 TYR Chi-restraints excluded: chain A residue 111 MET Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 147 ARG Chi-restraints excluded: chain B residue 35 SER Chi-restraints excluded: chain B residue 95 TYR Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 109 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 22 optimal weight: 9.9990 chunk 12 optimal weight: 0.9980 chunk 33 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 40 optimal weight: 8.9990 chunk 43 optimal weight: 3.9990 chunk 35 optimal weight: 7.9990 chunk 39 optimal weight: 30.0000 chunk 13 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 131 HIS B 133 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7207 moved from start: 0.4674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 3346 Z= 0.254 Angle : 0.486 4.757 4544 Z= 0.284 Chirality : 0.026 0.093 554 Planarity : 0.003 0.026 592 Dihedral : 6.553 55.156 503 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Rotamer: Outliers : 3.72 % Allowed : 12.84 % Favored : 83.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.85 (0.43), residues: 342 helix: 2.10 (0.26), residues: 320 sheet: None (None), residues: 0 loop : -1.26 (1.58), residues: 22 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 78 HIS 0.005 0.001 HIS B 131 PHE 0.008 0.003 PHE A 33 TYR 0.022 0.002 TYR A 95 ARG 0.002 0.000 ARG A 147 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 684 Ramachandran restraints generated. 342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 684 Ramachandran restraints generated. 342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 85 time to evaluate : 0.460 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 148 LYS cc_start: 0.9364 (mtpp) cc_final: 0.9080 (mmmt) outliers start: 11 outliers final: 11 residues processed: 92 average time/residue: 0.4864 time to fit residues: 51.2249 Evaluate side-chains 94 residues out of total 296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 83 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 95 TYR Chi-restraints excluded: chain A residue 111 MET Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 147 ARG Chi-restraints excluded: chain B residue 35 SER Chi-restraints excluded: chain B residue 95 TYR Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 109 SER Chi-restraints excluded: chain B residue 125 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 39 optimal weight: 30.0000 chunk 30 optimal weight: 3.9990 chunk 20 optimal weight: 0.6980 chunk 4 optimal weight: 4.9990 chunk 19 optimal weight: 0.6980 chunk 26 optimal weight: 0.9990 chunk 40 optimal weight: 7.9990 chunk 42 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 35 optimal weight: 7.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7205 moved from start: 0.5054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3346 Z= 0.249 Angle : 0.486 4.871 4544 Z= 0.282 Chirality : 0.026 0.096 554 Planarity : 0.002 0.023 592 Dihedral : 6.616 57.912 503 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Rotamer: Outliers : 4.73 % Allowed : 14.19 % Favored : 81.08 % 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: 3.02 (0.42), residues: 342 helix: 2.21 (0.26), residues: 320 sheet: None (None), residues: 0 loop : -1.24 (1.49), residues: 22 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 78 HIS 0.008 0.002 HIS B 131 PHE 0.016 0.005 PHE B 33 TYR 0.023 0.002 TYR A 95 ARG 0.002 0.000 ARG A 147 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 684 Ramachandran restraints generated. 342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 684 Ramachandran restraints generated. 342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 85 time to evaluate : 0.492 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 MET cc_start: 0.8316 (ttp) cc_final: 0.8018 (tmm) REVERT: B 95 TYR cc_start: 0.7854 (OUTLIER) cc_final: 0.6476 (t80) REVERT: B 148 LYS cc_start: 0.9326 (mtpp) cc_final: 0.9066 (mmmt) outliers start: 14 outliers final: 11 residues processed: 94 average time/residue: 0.4143 time to fit residues: 44.3750 Evaluate side-chains 95 residues out of total 296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 83 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 95 TYR Chi-restraints excluded: chain A residue 111 MET Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 147 ARG Chi-restraints excluded: chain B residue 35 SER Chi-restraints excluded: chain B residue 95 TYR Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 109 SER Chi-restraints excluded: chain B residue 125 SER Chi-restraints excluded: chain B residue 144 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 24 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 chunk 31 optimal weight: 6.9990 chunk 17 optimal weight: 0.8980 chunk 36 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 chunk 10 optimal weight: 0.5980 chunk 14 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 HIS B 131 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7180 moved from start: 0.5317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3346 Z= 0.204 Angle : 0.438 5.391 4544 Z= 0.255 Chirality : 0.025 0.116 554 Planarity : 0.002 0.018 592 Dihedral : 6.667 59.936 503 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Rotamer: Outliers : 4.39 % Allowed : 15.20 % Favored : 80.41 % 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: 3.32 (0.42), residues: 342 helix: 2.44 (0.26), residues: 321 sheet: None (None), residues: 0 loop : -2.02 (1.29), residues: 21 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 78 HIS 0.004 0.001 HIS B 131 PHE 0.026 0.006 PHE B 33 TYR 0.020 0.002 TYR A 95 ARG 0.002 0.000 ARG A 147 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 684 Ramachandran restraints generated. 342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 684 Ramachandran restraints generated. 342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 82 time to evaluate : 0.465 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 LYS cc_start: 0.8867 (mmmt) cc_final: 0.8628 (mptt) REVERT: B 20 ARG cc_start: 0.8491 (mtm-85) cc_final: 0.8262 (mmm-85) REVERT: B 95 TYR cc_start: 0.7861 (OUTLIER) cc_final: 0.6306 (t80) REVERT: B 148 LYS cc_start: 0.9337 (mtpp) cc_final: 0.9052 (mmmt) outliers start: 13 outliers final: 12 residues processed: 89 average time/residue: 0.4369 time to fit residues: 44.2724 Evaluate side-chains 94 residues out of total 296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 81 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 95 TYR Chi-restraints excluded: chain A residue 111 MET Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 147 ARG Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 35 SER Chi-restraints excluded: chain B residue 95 TYR Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 125 SER Chi-restraints excluded: chain B residue 144 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 24 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 35 optimal weight: 6.9990 chunk 19 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 14 optimal weight: 8.9990 chunk 22 optimal weight: 10.0000 chunk 41 optimal weight: 3.9990 chunk 4 optimal weight: 0.7980 chunk 31 optimal weight: 4.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- 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: 0.7215 moved from start: 0.5621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 3346 Z= 0.253 Angle : 0.486 4.890 4544 Z= 0.283 Chirality : 0.025 0.096 554 Planarity : 0.002 0.022 592 Dihedral : 6.613 57.367 503 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Rotamer: Outliers : 4.73 % Allowed : 16.22 % Favored : 79.05 % 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: 3.28 (0.42), residues: 342 helix: 2.40 (0.26), residues: 323 sheet: None (None), residues: 0 loop : -2.21 (1.40), residues: 19 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 78 HIS 0.003 0.001 HIS A 143 PHE 0.018 0.005 PHE B 33 TYR 0.021 0.002 TYR A 95 ARG 0.002 0.000 ARG A 147 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 684 Ramachandran restraints generated. 342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 684 Ramachandran restraints generated. 342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 82 time to evaluate : 0.487 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 LYS cc_start: 0.8815 (mmmt) cc_final: 0.8595 (mptt) REVERT: B 20 ARG cc_start: 0.8505 (mtm-85) cc_final: 0.8271 (mmm-85) REVERT: B 95 TYR cc_start: 0.7887 (OUTLIER) cc_final: 0.6562 (t80) REVERT: B 148 LYS cc_start: 0.9327 (mtpp) cc_final: 0.9043 (mmmt) outliers start: 14 outliers final: 13 residues processed: 90 average time/residue: 0.4295 time to fit residues: 44.1346 Evaluate side-chains 95 residues out of total 296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 81 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 95 TYR Chi-restraints excluded: chain A residue 111 MET Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 147 ARG Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 35 SER Chi-restraints excluded: chain B residue 95 TYR Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 109 SER Chi-restraints excluded: chain B residue 125 SER Chi-restraints excluded: chain B residue 144 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 24 optimal weight: 3.9990 chunk 35 optimal weight: 6.9990 chunk 23 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 19 optimal weight: 0.8980 chunk 16 optimal weight: 5.9990 chunk 12 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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: 0.7181 moved from start: 0.5766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3346 Z= 0.196 Angle : 0.435 5.580 4544 Z= 0.252 Chirality : 0.025 0.093 554 Planarity : 0.002 0.017 592 Dihedral : 6.574 57.303 503 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 4.05 % Allowed : 18.24 % Favored : 77.70 % 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: 3.69 (0.42), residues: 342 helix: 2.66 (0.26), residues: 323 sheet: None (None), residues: 0 loop : -2.08 (1.43), residues: 19 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 78 HIS 0.002 0.001 HIS B 131 PHE 0.012 0.004 PHE B 33 TYR 0.019 0.001 TYR A 95 ARG 0.002 0.000 ARG A 147 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 684 Ramachandran restraints generated. 342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 684 Ramachandran restraints generated. 342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 82 time to evaluate : 0.477 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 LYS cc_start: 0.8837 (mmmt) cc_final: 0.8605 (mptt) REVERT: B 20 ARG cc_start: 0.8477 (mtm-85) cc_final: 0.8260 (mmm-85) REVERT: B 95 TYR cc_start: 0.7797 (OUTLIER) cc_final: 0.6310 (t80) REVERT: B 103 MET cc_start: 0.8549 (mpp) cc_final: 0.8330 (mpp) REVERT: B 148 LYS cc_start: 0.9309 (mtpp) cc_final: 0.9023 (mmmt) outliers start: 12 outliers final: 11 residues processed: 88 average time/residue: 0.4764 time to fit residues: 48.1317 Evaluate side-chains 92 residues out of total 296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 80 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 95 TYR Chi-restraints excluded: chain A residue 111 MET Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 147 ARG Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 35 SER Chi-restraints excluded: chain B residue 95 TYR Chi-restraints excluded: chain B residue 125 SER Chi-restraints excluded: chain B residue 144 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 20 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 33 optimal weight: 9.9990 chunk 38 optimal weight: 3.9990 chunk 40 optimal weight: 10.0000 chunk 37 optimal weight: 3.9990 chunk 39 optimal weight: 30.0000 chunk 23 optimal weight: 1.9990 chunk 17 optimal weight: 4.9990 chunk 31 optimal weight: 7.9990 chunk 12 optimal weight: 0.8980 overall best weight: 1.9788 ------------------------------------------------------------------------------- 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: 0.7243 moved from start: 0.6067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 3346 Z= 0.293 Angle : 0.536 5.018 4544 Z= 0.312 Chirality : 0.027 0.097 554 Planarity : 0.003 0.043 592 Dihedral : 6.198 57.252 501 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 15.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 5.07 % Allowed : 17.57 % Favored : 77.36 % 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: 3.26 (0.42), residues: 342 helix: 2.38 (0.26), residues: 324 sheet: None (None), residues: 0 loop : -2.45 (1.47), residues: 18 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 78 HIS 0.003 0.001 HIS A 143 PHE 0.016 0.005 PHE A 33 TYR 0.022 0.002 TYR A 95 ARG 0.002 0.000 ARG B 21 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 684 Ramachandran restraints generated. 342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 684 Ramachandran restraints generated. 342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 81 time to evaluate : 0.545 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 LYS cc_start: 0.8829 (mmmt) cc_final: 0.8615 (mptt) REVERT: B 95 TYR cc_start: 0.7780 (OUTLIER) cc_final: 0.6470 (t80) REVERT: B 148 LYS cc_start: 0.9329 (mtpp) cc_final: 0.9041 (mmmt) outliers start: 15 outliers final: 14 residues processed: 91 average time/residue: 0.4400 time to fit residues: 45.7351 Evaluate side-chains 96 residues out of total 296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 81 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 95 TYR Chi-restraints excluded: chain A residue 111 MET Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain A residue 147 ARG Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 35 SER Chi-restraints excluded: chain B residue 95 TYR Chi-restraints excluded: chain B residue 109 SER Chi-restraints excluded: chain B residue 125 SER Chi-restraints excluded: chain B residue 144 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 35 optimal weight: 6.9990 chunk 37 optimal weight: 3.9990 chunk 39 optimal weight: 30.0000 chunk 25 optimal weight: 0.9980 chunk 41 optimal weight: 3.9990 chunk 19 optimal weight: 0.9990 chunk 29 optimal weight: 0.6980 chunk 43 optimal weight: 3.9990 chunk 40 optimal weight: 6.9990 chunk 34 optimal weight: 20.0000 chunk 3 optimal weight: 0.8980 overall best weight: 1.5184 ------------------------------------------------------------------------------- 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: 0.7216 moved from start: 0.6172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 3346 Z= 0.246 Angle : 0.499 5.604 4544 Z= 0.285 Chirality : 0.025 0.094 554 Planarity : 0.003 0.042 592 Dihedral : 6.264 59.289 501 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 5.07 % Allowed : 17.57 % Favored : 77.36 % 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: 3.38 (0.42), residues: 342 helix: 2.46 (0.26), residues: 324 sheet: None (None), residues: 0 loop : -2.46 (1.46), residues: 18 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 78 HIS 0.002 0.001 HIS A 143 PHE 0.017 0.005 PHE B 33 TYR 0.020 0.002 TYR A 95 ARG 0.002 0.000 ARG A 147 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 684 Ramachandran restraints generated. 342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 684 Ramachandran restraints generated. 342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 82 time to evaluate : 0.465 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 LYS cc_start: 0.8811 (mmmt) cc_final: 0.8604 (mptt) REVERT: B 20 ARG cc_start: 0.8482 (mtm-85) cc_final: 0.8245 (mmm-85) REVERT: B 95 TYR cc_start: 0.7790 (OUTLIER) cc_final: 0.6285 (t80) REVERT: B 148 LYS cc_start: 0.9323 (mtpp) cc_final: 0.9034 (mmmt) outliers start: 15 outliers final: 14 residues processed: 92 average time/residue: 0.4552 time to fit residues: 47.9681 Evaluate side-chains 97 residues out of total 296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 82 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 95 TYR Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 111 MET Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain A residue 147 ARG Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 35 SER Chi-restraints excluded: chain B residue 95 TYR Chi-restraints excluded: chain B residue 109 SER Chi-restraints excluded: chain B residue 125 SER Chi-restraints excluded: chain B residue 144 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 26 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 32 optimal weight: 6.9990 chunk 5 optimal weight: 6.9990 chunk 9 optimal weight: 0.7980 chunk 34 optimal weight: 20.0000 chunk 14 optimal weight: 4.9990 chunk 35 optimal weight: 6.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- 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: 0.7234 moved from start: 0.6262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 3346 Z= 0.270 Angle : 0.531 5.630 4544 Z= 0.304 Chirality : 0.026 0.097 554 Planarity : 0.003 0.042 592 Dihedral : 6.287 59.726 501 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 13.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 5.07 % Allowed : 17.57 % Favored : 77.36 % 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: 3.23 (0.42), residues: 342 helix: 2.37 (0.26), residues: 324 sheet: None (None), residues: 0 loop : -2.60 (1.38), residues: 18 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 102 HIS 0.002 0.001 HIS A 143 PHE 0.018 0.005 PHE B 33 TYR 0.021 0.002 TYR A 95 ARG 0.002 0.000 ARG B 21 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 684 Ramachandran restraints generated. 342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 684 Ramachandran restraints generated. 342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 83 time to evaluate : 0.478 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 LYS cc_start: 0.8818 (mmmt) cc_final: 0.8611 (mptt) REVERT: B 95 TYR cc_start: 0.7739 (OUTLIER) cc_final: 0.6175 (t80) REVERT: B 148 LYS cc_start: 0.9330 (mtpp) cc_final: 0.9027 (mmmt) outliers start: 15 outliers final: 14 residues processed: 93 average time/residue: 0.4648 time to fit residues: 49.5744 Evaluate side-chains 98 residues out of total 296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 83 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 95 TYR Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 111 MET Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain A residue 147 ARG Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 35 SER Chi-restraints excluded: chain B residue 95 TYR Chi-restraints excluded: chain B residue 109 SER Chi-restraints excluded: chain B residue 125 SER Chi-restraints excluded: chain B residue 144 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 4 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 30 optimal weight: 0.0970 chunk 1 optimal weight: 0.9990 chunk 25 optimal weight: 0.8980 chunk 40 optimal weight: 8.9990 chunk 23 optimal weight: 0.9990 chunk 29 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 chunk 26 optimal weight: 0.5980 chunk 17 optimal weight: 0.8980 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 133 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4539 r_free = 0.4539 target = 0.120931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.096704 restraints weight = 33534.539| |-----------------------------------------------------------------------------| r_work (start): 0.4127 rms_B_bonded: 3.75 r_work (final): 0.4127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7133 moved from start: 0.6407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3346 Z= 0.173 Angle : 0.439 6.172 4544 Z= 0.249 Chirality : 0.024 0.093 554 Planarity : 0.002 0.036 592 Dihedral : 6.239 59.223 501 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 3.72 % Allowed : 18.58 % Favored : 77.70 % 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: 3.73 (0.42), residues: 342 helix: 2.72 (0.26), residues: 325 sheet: None (None), residues: 0 loop : -3.43 (1.07), residues: 17 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 102 HIS 0.003 0.001 HIS B 131 PHE 0.005 0.002 PHE A 33 TYR 0.017 0.001 TYR A 95 ARG 0.002 0.000 ARG A 147 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2100.78 seconds wall clock time: 38 minutes 47.71 seconds (2327.71 seconds total)