Starting phenix.real_space_refine on Fri Dec 8 01:15:11 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e2j_27838/12_2023/8e2j_27838_trim.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e2j_27838/12_2023/8e2j_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_27838/12_2023/8e2j_27838.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e2j_27838/12_2023/8e2j_27838.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e2j_27838/12_2023/8e2j_27838_trim.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e2j_27838/12_2023/8e2j_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-1.21rc1-5172/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: 3.52, per 1000 atoms: 0.59 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: 5.13 Conformation dependent library (CDL) restraints added in 764.3 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: 0.48 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: 2.37 Time building geometry restraints manager: 5.33 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: 2620 17.77 - 35.54: 148 35.54 - 53.31: 34 53.31 - 71.08: 9 71.08 - 88.85: 9 Dihedral angle restraints: 2820 sinusoidal: 1332 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 2817 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: 3.010 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: 0.130 Extract box with map and model: 9.200 Check model and map are aligned: 0.100 Set scattering table: 0.060 Process input model: 24.920 Find NCS groups from input model: 0.270 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:3.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.120 ------------------------------------------------------------------------------- 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 : 0.461 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: 8 outliers final: 5 residues processed: 124 average time/residue: 0.4994 time to fit residues: 69.0318 Evaluate side-chains 97 residues out of total 296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 92 time to evaluate : 0.498 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2485 time to fit residues: 2.0791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.8980 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: 0.9990 chunk 20 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 chunk 39 optimal weight: 30.0000 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 HIS B 157 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7176 moved from start: 0.3989 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= 0.257 Angle : 0.514 4.622 4544 Z= 0.300 Chirality : 0.026 0.108 554 Planarity : 0.003 0.023 592 Dihedral : 3.636 14.573 490 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Rotamer: Outliers : 3.04 % Allowed : 10.81 % Favored : 86.15 % 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: 2.43 (0.42), residues: 342 helix: 1.82 (0.26), residues: 322 sheet: None (None), residues: 0 loop : -1.62 (1.52), residues: 20 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 78 HIS 0.003 0.001 HIS A 92 PHE 0.012 0.003 PHE A 33 TYR 0.030 0.002 TYR A 95 ARG 0.004 0.000 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: 9 poor density : 91 time to evaluate : 0.507 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 outliers start: 9 outliers final: 7 residues processed: 97 average time/residue: 0.4401 time to fit residues: 48.7462 Evaluate side-chains 88 residues out of total 296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 81 time to evaluate : 0.485 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 7 outliers final: 1 residues processed: 7 average time/residue: 0.0821 time to fit residues: 1.5508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 22 optimal weight: 10.0000 chunk 12 optimal weight: 0.7980 chunk 33 optimal weight: 8.9990 chunk 27 optimal weight: 0.5980 chunk 11 optimal weight: 0.9990 chunk 40 optimal weight: 10.0000 chunk 43 optimal weight: 3.9990 chunk 35 optimal weight: 8.9990 chunk 39 optimal weight: 20.0000 chunk 13 optimal weight: 0.9980 chunk 32 optimal weight: 6.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 131 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7184 moved from start: 0.4781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3346 Z= 0.247 Angle : 0.488 4.546 4544 Z= 0.285 Chirality : 0.025 0.096 554 Planarity : 0.002 0.019 592 Dihedral : 3.512 13.286 490 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Rotamer: Outliers : 1.69 % Allowed : 13.51 % Favored : 84.80 % 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: 3.12 (0.42), residues: 342 helix: 2.27 (0.26), residues: 320 sheet: None (None), residues: 0 loop : -1.12 (1.57), residues: 22 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 78 HIS 0.005 0.001 HIS B 131 PHE 0.014 0.005 PHE B 33 TYR 0.028 0.002 TYR A 95 ARG 0.001 0.000 ARG B 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 90 residues out of total 296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 85 time to evaluate : 0.445 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 outliers start: 5 outliers final: 3 residues processed: 87 average time/residue: 0.4724 time to fit residues: 46.5096 Evaluate side-chains 84 residues out of total 296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 81 time to evaluate : 0.470 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1060 time to fit residues: 1.0562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.5980 chunk 4 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 40 optimal weight: 8.9990 chunk 42 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 35 optimal weight: 8.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 0.7191 moved from start: 0.5086 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= 0.252 Angle : 0.500 5.175 4544 Z= 0.289 Chirality : 0.026 0.102 554 Planarity : 0.002 0.012 592 Dihedral : 3.468 13.103 490 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Rotamer: Outliers : 1.01 % Allowed : 17.57 % 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: 3.10 (0.42), residues: 342 helix: 2.26 (0.26), residues: 320 sheet: None (None), residues: 0 loop : -1.22 (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 0.022 0.006 PHE B 33 TYR 0.028 0.002 TYR A 95 ARG 0.002 0.000 ARG B 21 *********************** 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 86 residues out of total 296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 83 time to evaluate : 0.425 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 outliers start: 3 outliers final: 1 residues processed: 86 average time/residue: 0.4384 time to fit residues: 42.8592 Evaluate side-chains 83 residues out of total 296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 82 time to evaluate : 0.457 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0730 time to fit residues: 0.6933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.5980 chunk 36 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 chunk 8 optimal weight: 1.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 131 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7176 moved from start: 0.5464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3346 Z= 0.214 Angle : 0.449 4.924 4544 Z= 0.263 Chirality : 0.025 0.095 554 Planarity : 0.002 0.011 592 Dihedral : 3.397 12.610 490 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 1.35 % Allowed : 17.23 % 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: 3.27 (0.41), residues: 342 helix: 2.40 (0.25), residues: 321 sheet: None (None), residues: 0 loop : -2.02 (1.28), 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 0.018 0.005 PHE B 33 TYR 0.024 0.001 TYR A 95 ARG 0.004 0.000 ARG A 20 *********************** 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 87 residues out of total 296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 83 time to evaluate : 0.469 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 outliers start: 4 outliers final: 3 residues processed: 86 average time/residue: 0.3972 time to fit residues: 38.9138 Evaluate side-chains 81 residues out of total 296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 78 time to evaluate : 0.349 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0903 time to fit residues: 0.8791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 24 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 chunk 35 optimal weight: 7.9990 chunk 19 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 14 optimal weight: 5.9990 chunk 22 optimal weight: 7.9990 chunk 41 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 31 optimal weight: 5.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 0.7233 moved from start: 0.5836 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= 0.297 Angle : 0.549 4.635 4544 Z= 0.319 Chirality : 0.027 0.100 554 Planarity : 0.002 0.015 592 Dihedral : 3.451 12.084 490 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 13.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 1.01 % Allowed : 19.93 % 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: 2.91 (0.42), residues: 342 helix: 2.14 (0.26), residues: 322 sheet: None (None), residues: 0 loop : -1.60 (1.50), residues: 20 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 78 HIS 0.010 0.002 HIS B 131 PHE 0.017 0.005 PHE A 33 TYR 0.027 0.002 TYR A 95 ARG 0.002 0.000 ARG B 21 *********************** 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 83 residues out of total 296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 80 time to evaluate : 0.458 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 outliers start: 3 outliers final: 1 residues processed: 83 average time/residue: 0.4515 time to fit residues: 42.6881 Evaluate side-chains 81 residues out of total 296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 80 time to evaluate : 0.352 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0625 time to fit residues: 0.5385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.7980 chunk 42 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 chunk 19 optimal weight: 0.5980 chunk 16 optimal weight: 0.9990 chunk 12 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7160 moved from start: 0.5972 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= 0.181 Angle : 0.443 5.675 4544 Z= 0.255 Chirality : 0.025 0.114 554 Planarity : 0.002 0.010 592 Dihedral : 3.392 11.416 490 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Rotamer: Outliers : 1.69 % Allowed : 20.95 % 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: 3.36 (0.41), residues: 342 helix: 2.47 (0.26), residues: 323 sheet: None (None), residues: 0 loop : -2.71 (1.03), residues: 19 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 102 HIS 0.012 0.002 HIS B 131 PHE 0.007 0.004 PHE A 33 TYR 0.022 0.002 TYR A 95 ARG 0.001 0.000 ARG B 85 *********************** 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 87 residues out of total 296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 82 time to evaluate : 0.430 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 outliers start: 5 outliers final: 4 residues processed: 86 average time/residue: 0.4566 time to fit residues: 44.7313 Evaluate side-chains 86 residues out of total 296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 82 time to evaluate : 0.475 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1227 time to fit residues: 1.3766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 20 optimal weight: 0.0470 chunk 3 optimal weight: 1.9990 chunk 33 optimal weight: 7.9990 chunk 38 optimal weight: 3.9990 chunk 40 optimal weight: 9.9990 chunk 37 optimal weight: 3.9990 chunk 39 optimal weight: 30.0000 chunk 23 optimal weight: 0.9990 chunk 17 optimal weight: 0.5980 chunk 31 optimal weight: 0.5980 chunk 12 optimal weight: 0.9990 overall best weight: 0.6482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7141 moved from start: 0.6156 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= 0.169 Angle : 0.439 5.383 4544 Z= 0.255 Chirality : 0.024 0.094 554 Planarity : 0.002 0.009 592 Dihedral : 3.272 10.982 490 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 0.34 % Allowed : 22.64 % Favored : 77.03 % 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: 3.67 (0.41), residues: 342 helix: 2.66 (0.26), residues: 325 sheet: None (None), residues: 0 loop : -2.98 (1.11), residues: 17 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 102 HIS 0.013 0.002 HIS B 131 PHE 0.013 0.003 PHE B 33 TYR 0.021 0.002 TYR A 95 ARG 0.002 0.000 ARG B 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 82 residues out of total 296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 81 time to evaluate : 0.469 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 outliers start: 1 outliers final: 1 residues processed: 81 average time/residue: 0.5032 time to fit residues: 46.0641 Evaluate side-chains 81 residues out of total 296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 80 time to evaluate : 0.558 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0997 time to fit residues: 0.8781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 35 optimal weight: 7.9990 chunk 37 optimal weight: 4.9990 chunk 39 optimal weight: 30.0000 chunk 25 optimal weight: 0.8980 chunk 41 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 43 optimal weight: 4.9990 chunk 40 optimal weight: 6.9990 chunk 34 optimal weight: 20.0000 chunk 3 optimal weight: 1.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7234 moved from start: 0.6401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 3346 Z= 0.319 Angle : 0.594 7.412 4544 Z= 0.346 Chirality : 0.028 0.150 554 Planarity : 0.003 0.014 592 Dihedral : 3.315 11.335 490 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 14.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 1.01 % Allowed : 21.28 % 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: 3.16 (0.41), residues: 342 helix: 2.35 (0.26), residues: 318 sheet: None (None), residues: 0 loop : -1.80 (1.26), residues: 24 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 78 HIS 0.013 0.003 HIS B 131 PHE 0.018 0.005 PHE A 33 TYR 0.029 0.002 TYR A 95 ARG 0.005 0.001 ARG B 20 *********************** 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 84 residues out of total 296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 81 time to evaluate : 0.501 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 outliers start: 3 outliers final: 3 residues processed: 84 average time/residue: 0.4848 time to fit residues: 46.0587 Evaluate side-chains 83 residues out of total 296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 80 time to evaluate : 0.460 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.3125 time to fit residues: 1.6783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 26 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 chunk 37 optimal weight: 3.9990 chunk 10 optimal weight: 0.6980 chunk 32 optimal weight: 10.0000 chunk 5 optimal weight: 10.0000 chunk 9 optimal weight: 0.9990 chunk 34 optimal weight: 20.0000 chunk 14 optimal weight: 3.9990 chunk 35 optimal weight: 6.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7194 moved from start: 0.6423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 3346 Z= 0.234 Angle : 0.548 9.256 4544 Z= 0.304 Chirality : 0.026 0.124 554 Planarity : 0.002 0.010 592 Dihedral : 3.296 10.825 490 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 13.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Rotamer: Outliers : 0.00 % Allowed : 22.97 % Favored : 77.03 % 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: 3.31 (0.41), residues: 342 helix: 2.42 (0.26), residues: 323 sheet: None (None), residues: 0 loop : -2.35 (1.33), residues: 19 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 78 HIS 0.010 0.002 HIS B 131 PHE 0.018 0.005 PHE B 33 TYR 0.025 0.002 TYR A 95 ARG 0.002 0.000 ARG B 147 ********************** 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 81 residues out of total 296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 81 time to evaluate : 0.480 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 outliers start: 0 outliers final: 0 residues processed: 81 average time/residue: 0.5012 time to fit residues: 45.7676 Evaluate side-chains 80 residues out of total 296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 80 time to evaluate : 0.477 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 4 optimal weight: 3.9990 chunk 6 optimal weight: 0.9980 chunk 30 optimal weight: 0.8980 chunk 1 optimal weight: 0.5980 chunk 25 optimal weight: 0.9990 chunk 40 optimal weight: 8.9990 chunk 23 optimal weight: 0.0370 chunk 29 optimal weight: 0.8980 chunk 27 optimal weight: 0.6980 chunk 26 optimal weight: 0.5980 chunk 17 optimal weight: 0.5980 overall best weight: 0.5058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4565 r_free = 0.4565 target = 0.122692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.098883 restraints weight = 33880.929| |-----------------------------------------------------------------------------| r_work (start): 0.4129 rms_B_bonded: 3.79 r_work (final): 0.4129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7063 moved from start: 0.6577 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= 0.168 Angle : 0.465 6.520 4544 Z= 0.262 Chirality : 0.025 0.119 554 Planarity : 0.002 0.010 592 Dihedral : 3.247 10.712 490 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 0.00 % Allowed : 21.96 % 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 (0.41), residues: 342 helix: 2.68 (0.26), residues: 325 sheet: None (None), residues: 0 loop : -3.13 (1.09), residues: 17 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 102 HIS 0.011 0.002 HIS B 131 PHE 0.007 0.003 PHE A 33 TYR 0.022 0.002 TYR A 95 ARG 0.001 0.000 ARG B 85 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2160.16 seconds wall clock time: 39 minutes 53.40 seconds (2393.40 seconds total)