Starting phenix.real_space_refine on Tue Sep 24 01:01:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e2j_27838/09_2024/8e2j_27838_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e2j_27838/09_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_27838/09_2024/8e2j_27838.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e2j_27838/09_2024/8e2j_27838.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e2j_27838/09_2024/8e2j_27838_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e2j_27838/09_2024/8e2j_27838_trim.cif" } 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 Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 3.73, per 1000 atoms: 0.62 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 - 3.00 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 Time building additional restraints: 1.57 Conformation dependent library (CDL) restraints added in 361.1 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: 2.20 Time building geometry restraints manager: 1.86 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: 0.00 - 1.15: 9978 1.15 - 2.29: 645 2.29 - 3.44: 19 3.44 - 4.59: 5 4.59 - 5.73: 1 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: 2675 17.77 - 35.54: 152 35.54 - 53.31: 44 53.31 - 71.08: 12 71.08 - 88.85: 9 Dihedral angle restraints: 2892 sinusoidal: 1404 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 2889 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 2.450 nonbonded pdb=" O GLN B 61 " pdb=" HG SER B 64 " model vdw 1.559 2.450 nonbonded pdb=" O ARG B 21 " pdb=" HG SER B 24 " model vdw 1.606 2.450 nonbonded pdb="HH11 ARG B 129 " pdb=" OD1 ASN B 130 " model vdw 1.611 2.450 nonbonded pdb=" O GLN A 61 " pdb=" HG SER A 64 " model vdw 1.611 2.450 ... (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 Time spend for trying shortcut: 0.00 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: 2.350 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: 0.120 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 17.050 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.910 ------------------------------------------------------------------------------- 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 : 0.441 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: 0.4965 time to fit residues: 68.6967 Evaluate side-chains 97 residues out of total 296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 92 time to evaluate : 0.463 ------------------------------------------------------------------------------- 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: 6.9990 chunk 18 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 34 optimal weight: 20.0000 chunk 13 optimal weight: 0.1980 chunk 20 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 39 optimal weight: 30.0000 overall best weight: 1.7786 ------------------------------------------------------------------------------- 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: 0.7199 moved from start: 0.3984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 3346 Z= 0.287 Angle : 0.538 4.877 4544 Z= 0.312 Chirality : 0.027 0.107 554 Planarity : 0.003 0.030 592 Dihedral : 6.369 55.339 503 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Rotamer: Outliers : 2.36 % Allowed : 13.18 % Favored : 84.46 % 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: 2.36 (0.42), residues: 342 helix: 1.76 (0.26), residues: 320 sheet: None (None), residues: 0 loop : -1.05 (1.60), residues: 22 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 78 HIS 0.004 0.002 HIS A 131 PHE 0.013 0.004 PHE A 33 TYR 0.023 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 99 residues out of total 296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 92 time to evaluate : 0.422 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: B 81 ILE cc_start: 0.8900 (mt) cc_final: 0.8683 (mt) REVERT: B 114 GLU cc_start: 0.8637 (tp30) cc_final: 0.8387 (tp30) outliers start: 7 outliers final: 7 residues processed: 96 average time/residue: 0.4524 time to fit residues: 49.1215 Evaluate side-chains 91 residues out of total 296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 84 time to evaluate : 0.452 ------------------------------------------------------------------------------- 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 134 LEU 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 22 optimal weight: 3.9990 chunk 12 optimal weight: 0.8980 chunk 33 optimal weight: 5.9990 chunk 27 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 40 optimal weight: 8.9990 chunk 43 optimal weight: 3.9990 chunk 35 optimal weight: 8.9990 chunk 39 optimal weight: 20.0000 chunk 13 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- 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** ** A 143 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: 0.7233 moved from start: 0.4882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 3346 Z= 0.304 Angle : 0.532 4.581 4544 Z= 0.311 Chirality : 0.027 0.101 554 Planarity : 0.003 0.030 592 Dihedral : 6.491 57.899 503 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Rotamer: Outliers : 3.38 % Allowed : 14.86 % Favored : 81.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.78 (0.42), residues: 342 helix: 2.06 (0.26), residues: 320 sheet: None (None), residues: 0 loop : -1.33 (1.56), residues: 22 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 78 HIS 0.004 0.001 HIS B 131 PHE 0.013 0.003 PHE A 33 TYR 0.023 0.002 TYR A 95 ARG 0.003 0.001 ARG A 20 *********************** 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 93 residues out of total 296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 83 time to evaluate : 0.479 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: B 114 GLU cc_start: 0.8612 (tp30) cc_final: 0.8379 (tp30) REVERT: B 148 LYS cc_start: 0.9382 (mtpp) cc_final: 0.9083 (mmmt) outliers start: 10 outliers final: 9 residues processed: 89 average time/residue: 0.4564 time to fit residues: 45.9764 Evaluate side-chains 86 residues out of total 296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 77 time to evaluate : 0.476 ------------------------------------------------------------------------------- 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 95 TYR Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 144 GLN 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: 0.3980 chunk 20 optimal weight: 0.9980 chunk 4 optimal weight: 4.9990 chunk 19 optimal weight: 0.5980 chunk 26 optimal weight: 0.9990 chunk 40 optimal weight: 7.9990 chunk 42 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 11 optimal weight: 0.7980 chunk 35 optimal weight: 7.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7155 moved from start: 0.5176 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= 0.186 Angle : 0.430 5.152 4544 Z= 0.249 Chirality : 0.025 0.105 554 Planarity : 0.002 0.023 592 Dihedral : 6.562 59.060 503 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Rotamer: Outliers : 3.38 % Allowed : 15.20 % Favored : 81.42 % 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: 3.34 (0.42), residues: 342 helix: 2.46 (0.26), residues: 323 sheet: None (None), residues: 0 loop : -2.63 (1.11), residues: 19 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 0.006 0.002 PHE B 33 TYR 0.020 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 90 residues out of total 296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 80 time to evaluate : 0.448 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: B 81 ILE cc_start: 0.8858 (mt) cc_final: 0.8648 (mt) REVERT: B 95 TYR cc_start: 0.7817 (OUTLIER) cc_final: 0.6275 (t80) REVERT: B 131 HIS cc_start: 0.7547 (t-170) cc_final: 0.7160 (t-170) REVERT: B 148 LYS cc_start: 0.9344 (mtpp) cc_final: 0.9059 (mmmt) outliers start: 10 outliers final: 8 residues processed: 87 average time/residue: 0.4850 time to fit residues: 47.3417 Evaluate side-chains 86 residues out of total 296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 77 time to evaluate : 0.446 ------------------------------------------------------------------------------- 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 134 LEU Chi-restraints excluded: chain A residue 147 ARG Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 95 TYR Chi-restraints excluded: chain B residue 98 LEU 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: 4.9990 chunk 0 optimal weight: 3.9990 chunk 31 optimal weight: 5.9990 chunk 17 optimal weight: 2.9990 chunk 36 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 38 optimal weight: 3.9990 chunk 10 optimal weight: 0.5980 chunk 14 optimal weight: 6.9990 chunk 8 optimal weight: 1.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7231 moved from start: 0.5581 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= 0.292 Angle : 0.521 4.697 4544 Z= 0.304 Chirality : 0.027 0.097 554 Planarity : 0.003 0.026 592 Dihedral : 6.462 55.632 503 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Rotamer: Outliers : 2.36 % Allowed : 16.89 % Favored : 80.74 % 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: 3.36 (0.42), residues: 342 helix: 2.44 (0.26), residues: 320 sheet: None (None), residues: 0 loop : -1.31 (1.42), residues: 22 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 78 HIS 0.004 0.002 HIS B 131 PHE 0.017 0.004 PHE A 33 TYR 0.022 0.002 TYR A 95 ARG 0.003 0.000 ARG B 21 *********************** 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 88 residues out of total 296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 81 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: B 95 TYR cc_start: 0.7880 (OUTLIER) cc_final: 0.6507 (t80) REVERT: B 114 GLU cc_start: 0.8583 (tp30) cc_final: 0.8364 (tp30) REVERT: B 148 LYS cc_start: 0.9364 (mtpp) cc_final: 0.9076 (mmmt) outliers start: 7 outliers final: 6 residues processed: 86 average time/residue: 0.4688 time to fit residues: 45.5176 Evaluate side-chains 87 residues out of total 296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 80 time to evaluate : 0.411 ------------------------------------------------------------------------------- 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 134 LEU Chi-restraints excluded: chain A residue 147 ARG Chi-restraints excluded: chain B residue 95 TYR 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: 3.9990 chunk 10 optimal weight: 0.7980 chunk 42 optimal weight: 2.9990 chunk 35 optimal weight: 6.9990 chunk 19 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 14 optimal weight: 6.9990 chunk 22 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 31 optimal weight: 0.8980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7170 moved from start: 0.5801 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= 0.190 Angle : 0.426 5.696 4544 Z= 0.247 Chirality : 0.025 0.093 554 Planarity : 0.002 0.019 592 Dihedral : 6.034 55.737 501 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 2.36 % Allowed : 17.91 % Favored : 79.73 % 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: 3.82 (0.41), residues: 342 helix: 2.76 (0.26), residues: 321 sheet: None (None), residues: 0 loop : -1.80 (1.33), residues: 21 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 78 HIS 0.004 0.001 HIS B 131 PHE 0.006 0.002 PHE A 33 TYR 0.019 0.001 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 86 residues out of total 296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 79 time to evaluate : 0.495 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: 0.8899 (mmmt) cc_final: 0.8648 (mptt) REVERT: B 95 TYR cc_start: 0.7832 (OUTLIER) cc_final: 0.6355 (t80) REVERT: B 148 LYS cc_start: 0.9342 (mtpp) cc_final: 0.9069 (mmmt) outliers start: 7 outliers final: 5 residues processed: 84 average time/residue: 0.4729 time to fit residues: 44.9453 Evaluate side-chains 83 residues out of total 296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 77 time to evaluate : 0.463 ------------------------------------------------------------------------------- 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 134 LEU Chi-restraints excluded: chain B residue 95 TYR 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: 4.9990 chunk 35 optimal weight: 6.9990 chunk 23 optimal weight: 0.9980 chunk 42 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 25 optimal weight: 0.5980 chunk 19 optimal weight: 0.5980 chunk 16 optimal weight: 4.9990 chunk 12 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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: 0.7175 moved from start: 0.6014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3346 Z= 0.198 Angle : 0.443 5.602 4544 Z= 0.255 Chirality : 0.025 0.131 554 Planarity : 0.002 0.015 592 Dihedral : 5.435 57.328 497 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 2.36 % Allowed : 19.26 % Favored : 78.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.03 (0.41), residues: 342 helix: 2.88 (0.26), residues: 321 sheet: None (None), residues: 0 loop : -1.66 (1.32), residues: 21 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 78 HIS 0.003 0.001 HIS A 143 PHE 0.010 0.003 PHE A 33 TYR 0.019 0.001 TYR A 95 ARG 0.001 0.000 ARG B 21 *********************** 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 85 residues out of total 296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 78 time to evaluate : 0.414 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: B 81 ILE cc_start: 0.8849 (mt) cc_final: 0.8640 (mt) REVERT: B 95 TYR cc_start: 0.7672 (OUTLIER) cc_final: 0.6205 (t80) REVERT: B 114 GLU cc_start: 0.8430 (tp30) cc_final: 0.8214 (tp30) REVERT: B 148 LYS cc_start: 0.9341 (mtpp) cc_final: 0.9054 (mmmt) outliers start: 7 outliers final: 6 residues processed: 83 average time/residue: 0.4767 time to fit residues: 44.6183 Evaluate side-chains 85 residues out of total 296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 78 time to evaluate : 0.455 ------------------------------------------------------------------------------- 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 134 LEU Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 95 TYR 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: 1.9990 chunk 33 optimal weight: 8.9990 chunk 38 optimal weight: 3.9990 chunk 40 optimal weight: 8.9990 chunk 37 optimal weight: 3.9990 chunk 39 optimal weight: 20.0000 chunk 23 optimal weight: 4.9990 chunk 17 optimal weight: 2.9990 chunk 31 optimal weight: 5.9990 chunk 12 optimal weight: 0.5980 overall best weight: 2.3188 ------------------------------------------------------------------------------- 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: 0.7244 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 : 0.005 0.038 3346 Z= 0.332 Angle : 0.565 5.638 4544 Z= 0.326 Chirality : 0.028 0.105 554 Planarity : 0.003 0.021 592 Dihedral : 5.466 57.194 497 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 3.38 % Allowed : 18.58 % Favored : 78.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.39 (0.42), residues: 342 helix: 2.45 (0.26), residues: 324 sheet: None (None), residues: 0 loop : -2.23 (1.39), residues: 18 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 78 HIS 0.003 0.001 HIS A 92 PHE 0.019 0.005 PHE A 33 TYR 0.023 0.002 TYR A 95 ARG 0.003 0.000 ARG A 147 *********************** 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 89 residues out of total 296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 79 time to evaluate : 0.454 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: B 81 ILE cc_start: 0.8892 (mt) cc_final: 0.8688 (mt) REVERT: B 95 TYR cc_start: 0.7770 (OUTLIER) cc_final: 0.6445 (t80) REVERT: B 114 GLU cc_start: 0.8588 (tp30) cc_final: 0.8329 (tp30) REVERT: B 148 LYS cc_start: 0.9381 (mtpp) cc_final: 0.9094 (mmmt) outliers start: 10 outliers final: 9 residues processed: 86 average time/residue: 0.4716 time to fit residues: 45.8478 Evaluate side-chains 87 residues out of total 296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 77 time to evaluate : 0.461 ------------------------------------------------------------------------------- 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 134 LEU Chi-restraints excluded: chain A residue 147 ARG Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 95 TYR Chi-restraints excluded: chain B residue 144 GLN Chi-restraints excluded: chain B residue 145 LEU 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: 0.2980 chunk 41 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 29 optimal weight: 0.5980 chunk 43 optimal weight: 2.9990 chunk 40 optimal weight: 6.9990 chunk 34 optimal weight: 20.0000 chunk 3 optimal weight: 1.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- 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: 0.7198 moved from start: 0.6259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3346 Z= 0.229 Angle : 0.475 5.861 4544 Z= 0.274 Chirality : 0.025 0.094 554 Planarity : 0.002 0.020 592 Dihedral : 5.527 59.916 497 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 2.36 % Allowed : 19.59 % Favored : 78.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.70 (0.42), residues: 342 helix: 2.65 (0.26), residues: 324 sheet: None (None), residues: 0 loop : -2.06 (1.47), residues: 18 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 78 HIS 0.002 0.001 HIS B 131 PHE 0.011 0.003 PHE A 33 TYR 0.020 0.002 TYR A 95 ARG 0.001 0.000 ARG B 21 *********************** 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 86 residues out of total 296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 79 time to evaluate : 0.511 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 59 TYR cc_start: 0.8125 (m-80) cc_final: 0.7690 (m-10) REVERT: B 81 ILE cc_start: 0.8859 (mt) cc_final: 0.8655 (mt) REVERT: B 95 TYR cc_start: 0.7735 (OUTLIER) cc_final: 0.5845 (t80) REVERT: B 114 GLU cc_start: 0.8575 (tp30) cc_final: 0.8343 (tp30) REVERT: B 148 LYS cc_start: 0.9345 (mtpp) cc_final: 0.9050 (mmmt) outliers start: 7 outliers final: 6 residues processed: 84 average time/residue: 0.4692 time to fit residues: 44.5174 Evaluate side-chains 86 residues out of total 296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 79 time to evaluate : 0.431 ------------------------------------------------------------------------------- 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 134 LEU Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 95 TYR 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: 1.9990 chunk 21 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 37 optimal weight: 4.9990 chunk 10 optimal weight: 0.7980 chunk 32 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 9 optimal weight: 0.5980 chunk 34 optimal weight: 20.0000 chunk 14 optimal weight: 1.9990 chunk 35 optimal weight: 6.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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: 0.7182 moved from start: 0.6370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3346 Z= 0.202 Angle : 0.456 6.053 4544 Z= 0.262 Chirality : 0.025 0.097 554 Planarity : 0.002 0.022 592 Dihedral : 5.464 58.411 497 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 2.36 % Allowed : 19.26 % Favored : 78.38 % 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: 3.96 (0.41), residues: 342 helix: 2.82 (0.25), residues: 324 sheet: None (None), residues: 0 loop : -1.97 (1.50), residues: 18 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 78 HIS 0.003 0.001 HIS B 131 PHE 0.010 0.003 PHE A 33 TYR 0.019 0.001 TYR A 95 ARG 0.001 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 86 residues out of total 296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 79 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: A 28 ASP cc_start: 0.7389 (p0) cc_final: 0.6929 (t0) REVERT: A 59 TYR cc_start: 0.8133 (m-80) cc_final: 0.7675 (m-10) REVERT: B 81 ILE cc_start: 0.8851 (mt) cc_final: 0.8621 (mt) REVERT: B 95 TYR cc_start: 0.7550 (OUTLIER) cc_final: 0.5544 (t80) REVERT: B 114 GLU cc_start: 0.8549 (tp30) cc_final: 0.8325 (tp30) REVERT: B 148 LYS cc_start: 0.9332 (mtpp) cc_final: 0.9050 (mmmt) outliers start: 7 outliers final: 6 residues processed: 84 average time/residue: 0.4736 time to fit residues: 44.9535 Evaluate side-chains 86 residues out of total 296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 79 time to evaluate : 0.448 ------------------------------------------------------------------------------- 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 134 LEU Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 95 TYR 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: 0.6980 chunk 6 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 25 optimal weight: 0.6980 chunk 40 optimal weight: 8.9990 chunk 23 optimal weight: 0.1980 chunk 29 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.4556 r_free = 0.4556 target = 0.121537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.097361 restraints weight = 33297.909| |-----------------------------------------------------------------------------| r_work (start): 0.4153 rms_B_bonded: 3.80 r_work (final): 0.4153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7120 moved from start: 0.6502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3346 Z= 0.169 Angle : 0.434 6.214 4544 Z= 0.246 Chirality : 0.025 0.096 554 Planarity : 0.002 0.018 592 Dihedral : 5.439 56.738 497 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 2.36 % Allowed : 19.26 % Favored : 78.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.34 (0.41), residues: 342 helix: 3.11 (0.25), residues: 322 sheet: None (None), residues: 0 loop : -2.27 (1.11), residues: 20 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 102 HIS 0.003 0.001 HIS B 131 PHE 0.006 0.002 PHE A 33 TYR 0.017 0.001 TYR A 95 ARG 0.002 0.000 ARG B 85 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2035.96 seconds wall clock time: 35 minutes 59.22 seconds (2159.22 seconds total)