Starting phenix.real_space_refine on Sun Mar 10 18:49:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ynl_33965/03_2024/7ynl_33965_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ynl_33965/03_2024/7ynl_33965.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ynl_33965/03_2024/7ynl_33965_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ynl_33965/03_2024/7ynl_33965_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ynl_33965/03_2024/7ynl_33965_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ynl_33965/03_2024/7ynl_33965.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ynl_33965/03_2024/7ynl_33965.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ynl_33965/03_2024/7ynl_33965_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ynl_33965/03_2024/7ynl_33965_updated.pdb" } resolution = 2.6 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 64 5.16 5 C 2504 2.51 5 N 656 2.21 5 O 856 1.98 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-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 4080 Number of models: 1 Model: "" Number of chains: 16 Chain: "E" Number of atoms: 394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 394 Classifications: {'peptide': 58} Link IDs: {'TRANS': 57} Chain: "F" Number of atoms: 394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 394 Classifications: {'peptide': 58} Link IDs: {'TRANS': 57} Chain: "G" Number of atoms: 394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 394 Classifications: {'peptide': 58} Link IDs: {'TRANS': 57} Chain: "A" Number of atoms: 394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 394 Classifications: {'peptide': 58} Link IDs: {'TRANS': 57} Chain: "H" Number of atoms: 394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 394 Classifications: {'peptide': 58} Link IDs: {'TRANS': 57} Chain: "B" Number of atoms: 394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 394 Classifications: {'peptide': 58} Link IDs: {'TRANS': 57} Chain: "C" Number of atoms: 394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 394 Classifications: {'peptide': 58} Link IDs: {'TRANS': 57} Chain: "D" Number of atoms: 394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 394 Classifications: {'peptide': 58} Link IDs: {'TRANS': 57} Chain: "E" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 116 Unusual residues: {'IZ8': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 174 Unusual residues: {'IZ8': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 58 Unusual residues: {'IZ8': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 116 Unusual residues: {'IZ8': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 116 Unusual residues: {'IZ8': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 232 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 232 Unusual residues: {'IZ8': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 58 Unusual residues: {'IZ8': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 58 Unusual residues: {'IZ8': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.29, per 1000 atoms: 0.56 Number of scatterers: 4080 At special positions: 0 Unit cell: (86.32, 102.09, 37.35, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 64 16.00 O 856 8.00 N 656 7.00 C 2504 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.53 Conformation dependent library (CDL) restraints added in 763.4 milliseconds 896 Ramachandran restraints generated. 448 Oldfield, 0 Emsley, 448 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 784 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 0 helices and 0 sheets defined 0.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.55 Creating SS restraints... No hydrogen bonds 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: 0.00 Time building geometry restraints manager: 1.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1027 1.33 - 1.45: 1001 1.45 - 1.57: 2076 1.57 - 1.70: 0 1.70 - 1.82: 64 Bond restraints: 4168 Sorted by residual: bond pdb=" CA GLY H 86 " pdb=" C GLY H 86 " ideal model delta sigma weight residual 1.521 1.503 0.018 1.28e-02 6.10e+03 1.92e+00 bond pdb=" CA GLY D 86 " pdb=" C GLY D 86 " ideal model delta sigma weight residual 1.521 1.504 0.017 1.28e-02 6.10e+03 1.83e+00 bond pdb=" CA GLY G 86 " pdb=" C GLY G 86 " ideal model delta sigma weight residual 1.521 1.504 0.017 1.28e-02 6.10e+03 1.79e+00 bond pdb=" CA GLY F 86 " pdb=" C GLY F 86 " ideal model delta sigma weight residual 1.521 1.504 0.017 1.28e-02 6.10e+03 1.77e+00 bond pdb=" CA GLY C 86 " pdb=" C GLY C 86 " ideal model delta sigma weight residual 1.521 1.504 0.017 1.28e-02 6.10e+03 1.71e+00 ... (remaining 4163 not shown) Histogram of bond angle deviations from ideal: 101.03 - 107.08: 105 107.08 - 113.12: 2301 113.12 - 119.17: 740 119.17 - 125.22: 2710 125.22 - 131.26: 8 Bond angle restraints: 5864 Sorted by residual: angle pdb=" C39 IZ8 B 204 " pdb=" C40 IZ8 B 204 " pdb=" O41 IZ8 B 204 " ideal model delta sigma weight residual 99.26 120.06 -20.80 3.00e+00 1.11e-01 4.81e+01 angle pdb=" C39 IZ8 D 201 " pdb=" C40 IZ8 D 201 " pdb=" O41 IZ8 D 201 " ideal model delta sigma weight residual 99.26 120.05 -20.79 3.00e+00 1.11e-01 4.80e+01 angle pdb=" C39 IZ8 F 202 " pdb=" C40 IZ8 F 202 " pdb=" O41 IZ8 F 202 " ideal model delta sigma weight residual 99.26 120.05 -20.79 3.00e+00 1.11e-01 4.80e+01 angle pdb=" C42 IZ8 D 201 " pdb=" C40 IZ8 D 201 " pdb=" O41 IZ8 D 201 " ideal model delta sigma weight residual 140.54 119.76 20.78 3.00e+00 1.11e-01 4.80e+01 angle pdb=" C39 IZ8 H 202 " pdb=" C40 IZ8 H 202 " pdb=" O41 IZ8 H 202 " ideal model delta sigma weight residual 99.26 120.03 -20.77 3.00e+00 1.11e-01 4.79e+01 ... (remaining 5859 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.32: 1752 16.32 - 32.64: 112 32.64 - 48.96: 24 48.96 - 65.29: 15 65.29 - 81.61: 17 Dihedral angle restraints: 1920 sinusoidal: 680 harmonic: 1240 Sorted by residual: dihedral pdb=" CA VAL G 82 " pdb=" C VAL G 82 " pdb=" N GLU G 83 " pdb=" CA GLU G 83 " ideal model delta harmonic sigma weight residual -180.00 -160.74 -19.26 0 5.00e+00 4.00e-02 1.48e+01 dihedral pdb=" CA VAL E 82 " pdb=" C VAL E 82 " pdb=" N GLU E 83 " pdb=" CA GLU E 83 " ideal model delta harmonic sigma weight residual 180.00 -160.74 -19.26 0 5.00e+00 4.00e-02 1.48e+01 dihedral pdb=" CA VAL B 82 " pdb=" C VAL B 82 " pdb=" N GLU B 83 " pdb=" CA GLU B 83 " ideal model delta harmonic sigma weight residual -180.00 -160.75 -19.25 0 5.00e+00 4.00e-02 1.48e+01 ... (remaining 1917 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 210 0.028 - 0.055: 152 0.055 - 0.083: 94 0.083 - 0.110: 66 0.110 - 0.138: 46 Chirality restraints: 568 Sorted by residual: chirality pdb=" CA VAL E 82 " pdb=" N VAL E 82 " pdb=" C VAL E 82 " pdb=" CB VAL E 82 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.75e-01 chirality pdb=" CA VAL H 82 " pdb=" N VAL H 82 " pdb=" C VAL H 82 " pdb=" CB VAL H 82 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.67e-01 chirality pdb=" CA VAL G 82 " pdb=" N VAL G 82 " pdb=" C VAL G 82 " pdb=" CB VAL G 82 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.64e-01 ... (remaining 565 not shown) Planarity restraints: 592 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C11 IZ8 H 202 " 0.168 2.00e-02 2.50e+03 2.42e-01 2.35e+03 pdb=" C12 IZ8 H 202 " 0.183 2.00e-02 2.50e+03 pdb=" C14 IZ8 H 202 " 0.170 2.00e-02 2.50e+03 pdb=" C15 IZ8 H 202 " 0.037 2.00e-02 2.50e+03 pdb=" C17 IZ8 H 202 " -0.123 2.00e-02 2.50e+03 pdb=" C22 IZ8 H 202 " -0.152 2.00e-02 2.50e+03 pdb=" C23 IZ8 H 202 " -0.019 2.00e-02 2.50e+03 pdb=" C28 IZ8 H 202 " 0.142 2.00e-02 2.50e+03 pdb=" C29 IZ8 H 202 " 0.126 2.00e-02 2.50e+03 pdb=" C30 IZ8 H 202 " 0.139 2.00e-02 2.50e+03 pdb=" N09 IZ8 H 202 " -0.773 2.00e-02 2.50e+03 pdb=" N10 IZ8 H 202 " 0.084 2.00e-02 2.50e+03 pdb=" N16 IZ8 H 202 " 0.017 2.00e-02 2.50e+03 pdb=" O13 IZ8 H 202 " 0.289 2.00e-02 2.50e+03 pdb=" S18 IZ8 H 202 " -0.255 2.00e-02 2.50e+03 pdb=" S24 IZ8 H 202 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C11 IZ8 B 204 " 0.167 2.00e-02 2.50e+03 2.42e-01 2.35e+03 pdb=" C12 IZ8 B 204 " 0.183 2.00e-02 2.50e+03 pdb=" C14 IZ8 B 204 " 0.170 2.00e-02 2.50e+03 pdb=" C15 IZ8 B 204 " 0.036 2.00e-02 2.50e+03 pdb=" C17 IZ8 B 204 " -0.123 2.00e-02 2.50e+03 pdb=" C22 IZ8 B 204 " -0.152 2.00e-02 2.50e+03 pdb=" C23 IZ8 B 204 " -0.019 2.00e-02 2.50e+03 pdb=" C28 IZ8 B 204 " 0.142 2.00e-02 2.50e+03 pdb=" C29 IZ8 B 204 " 0.127 2.00e-02 2.50e+03 pdb=" C30 IZ8 B 204 " 0.139 2.00e-02 2.50e+03 pdb=" N09 IZ8 B 204 " -0.773 2.00e-02 2.50e+03 pdb=" N10 IZ8 B 204 " 0.084 2.00e-02 2.50e+03 pdb=" N16 IZ8 B 204 " 0.017 2.00e-02 2.50e+03 pdb=" O13 IZ8 B 204 " 0.289 2.00e-02 2.50e+03 pdb=" S18 IZ8 B 204 " -0.255 2.00e-02 2.50e+03 pdb=" S24 IZ8 B 204 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C11 IZ8 F 202 " 0.167 2.00e-02 2.50e+03 2.42e-01 2.35e+03 pdb=" C12 IZ8 F 202 " 0.183 2.00e-02 2.50e+03 pdb=" C14 IZ8 F 202 " 0.170 2.00e-02 2.50e+03 pdb=" C15 IZ8 F 202 " 0.037 2.00e-02 2.50e+03 pdb=" C17 IZ8 F 202 " -0.123 2.00e-02 2.50e+03 pdb=" C22 IZ8 F 202 " -0.153 2.00e-02 2.50e+03 pdb=" C23 IZ8 F 202 " -0.019 2.00e-02 2.50e+03 pdb=" C28 IZ8 F 202 " 0.142 2.00e-02 2.50e+03 pdb=" C29 IZ8 F 202 " 0.126 2.00e-02 2.50e+03 pdb=" C30 IZ8 F 202 " 0.139 2.00e-02 2.50e+03 pdb=" N09 IZ8 F 202 " -0.773 2.00e-02 2.50e+03 pdb=" N10 IZ8 F 202 " 0.083 2.00e-02 2.50e+03 pdb=" N16 IZ8 F 202 " 0.017 2.00e-02 2.50e+03 pdb=" O13 IZ8 F 202 " 0.289 2.00e-02 2.50e+03 pdb=" S18 IZ8 F 202 " -0.255 2.00e-02 2.50e+03 pdb=" S24 IZ8 F 202 " -0.032 2.00e-02 2.50e+03 ... (remaining 589 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 198 2.68 - 3.24: 4061 3.24 - 3.79: 5740 3.79 - 4.35: 7814 4.35 - 4.90: 14629 Nonbonded interactions: 32442 Sorted by model distance: nonbonded pdb=" NE2 GLN G 62 " pdb=" OG1 THR G 64 " model vdw 2.128 2.520 nonbonded pdb=" NE2 GLN C 62 " pdb=" OG1 THR C 64 " model vdw 2.128 2.520 nonbonded pdb=" NE2 GLN E 62 " pdb=" OG1 THR E 64 " model vdw 2.129 2.520 nonbonded pdb=" NE2 GLN F 62 " pdb=" OG1 THR F 64 " model vdw 2.129 2.520 nonbonded pdb=" NE2 GLN D 62 " pdb=" OG1 THR D 64 " model vdw 2.129 2.520 ... (remaining 32437 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' and (resid 40 through 97 or resid 201)) selection = (chain 'B' and (resid 40 through 97 or resid 201)) selection = chain 'C' selection = chain 'D' selection = (chain 'E' and (resid 40 through 97 or resid 201)) selection = (chain 'F' and (resid 40 through 97 or resid 201)) selection = chain 'G' selection = (chain 'H' and (resid 40 through 97 or resid 201)) } 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: 2.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 9.120 Check model and map are aligned: 0.070 Set scattering table: 0.040 Process input model: 14.260 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:12.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3213 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 : 0.009 0.043 4168 Z= 0.406 Angle : 2.400 20.802 5864 Z= 0.862 Chirality : 0.060 0.138 568 Planarity : 0.047 0.242 592 Dihedral : 16.151 81.607 1136 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 26.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.93 % Favored : 91.07 % Rotamer: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % 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: -6.11 (0.18), residues: 448 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.65 (0.14), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.002 HIS F 50 PHE 0.011 0.003 PHE E 94 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 896 Ramachandran restraints generated. 448 Oldfield, 0 Emsley, 448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 896 Ramachandran restraints generated. 448 Oldfield, 0 Emsley, 448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 0.362 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 94 PHE cc_start: 0.6193 (m-80) cc_final: 0.5990 (p90) REVERT: G 43 LYS cc_start: 0.6774 (mttt) cc_final: 0.6444 (pmtt) REVERT: B 80 LYS cc_start: 0.6153 (tptm) cc_final: 0.5075 (tmmt) outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 1.0065 time to fit residues: 85.6735 Evaluate side-chains 32 residues out of total 320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 32 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 5.9990 chunk 30 optimal weight: 6.9990 chunk 16 optimal weight: 9.9990 chunk 10 optimal weight: 10.0000 chunk 20 optimal weight: 10.0000 chunk 31 optimal weight: 6.9990 chunk 12 optimal weight: 4.9990 chunk 19 optimal weight: 0.7980 chunk 23 optimal weight: 0.8980 chunk 36 optimal weight: 3.9990 chunk 11 optimal weight: 0.8980 overall best weight: 2.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 50 HIS ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 50 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3803 moved from start: 0.6296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 4168 Z= 0.305 Angle : 1.520 31.762 5864 Z= 0.570 Chirality : 0.055 0.151 568 Planarity : 0.009 0.056 592 Dihedral : 16.644 87.931 520 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 6.88 % Allowed : 14.69 % Favored : 78.44 % 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: -4.99 (0.27), residues: 448 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.80 (0.21), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS H 50 PHE 0.022 0.002 PHE E 94 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 896 Ramachandran restraints generated. 448 Oldfield, 0 Emsley, 448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 896 Ramachandran restraints generated. 448 Oldfield, 0 Emsley, 448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 49 time to evaluate : 0.367 Fit side-chains revert: symmetry clash REVERT: E 94 PHE cc_start: 0.6300 (m-80) cc_final: 0.5973 (m-10) REVERT: G 46 GLU cc_start: 0.4300 (tp30) cc_final: 0.4093 (mm-30) REVERT: H 94 PHE cc_start: 0.6444 (m-80) cc_final: 0.5896 (m-80) REVERT: C 43 LYS cc_start: 0.3291 (OUTLIER) cc_final: 0.2854 (pptt) REVERT: C 61 GLU cc_start: 0.6469 (tt0) cc_final: 0.6252 (tt0) REVERT: C 82 VAL cc_start: 0.7332 (OUTLIER) cc_final: 0.7001 (p) outliers start: 22 outliers final: 12 residues processed: 68 average time/residue: 1.0855 time to fit residues: 76.5763 Evaluate side-chains 49 residues out of total 320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 35 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain G residue 82 VAL Chi-restraints excluded: chain G residue 92 THR Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain C residue 43 LYS Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 82 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 30 optimal weight: 8.9990 chunk 24 optimal weight: 9.9990 chunk 10 optimal weight: 10.0000 chunk 36 optimal weight: 6.9990 chunk 39 optimal weight: 3.9990 chunk 32 optimal weight: 10.0000 chunk 12 optimal weight: 9.9990 chunk 29 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 27 optimal weight: 7.9990 chunk 18 optimal weight: 8.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 62 GLN ** H 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 50 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4170 moved from start: 0.8846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.056 4168 Z= 0.310 Angle : 1.255 33.444 5864 Z= 0.529 Chirality : 0.061 0.207 568 Planarity : 0.006 0.050 592 Dihedral : 16.226 87.828 520 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 16.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.94 % Favored : 89.06 % Rotamer: Outliers : 9.69 % Allowed : 19.06 % Favored : 71.25 % 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: -4.79 (0.29), residues: 448 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.65 (0.22), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.002 HIS C 50 PHE 0.013 0.003 PHE C 94 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 896 Ramachandran restraints generated. 448 Oldfield, 0 Emsley, 448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 896 Ramachandran restraints generated. 448 Oldfield, 0 Emsley, 448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 44 time to evaluate : 0.386 Fit side-chains revert: symmetry clash REVERT: A 45 LYS cc_start: 0.7196 (OUTLIER) cc_final: 0.6617 (tppt) REVERT: H 83 GLU cc_start: 0.7590 (tp30) cc_final: 0.6997 (tp30) REVERT: H 94 PHE cc_start: 0.6672 (m-80) cc_final: 0.6262 (m-80) REVERT: B 50 HIS cc_start: 0.5381 (p90) cc_final: 0.4634 (m170) REVERT: C 46 GLU cc_start: 0.5702 (OUTLIER) cc_final: 0.5274 (mt-10) REVERT: C 97 LYS cc_start: 0.6834 (tttt) cc_final: 0.5633 (ttmt) outliers start: 31 outliers final: 21 residues processed: 70 average time/residue: 1.0476 time to fit residues: 76.0681 Evaluate side-chains 53 residues out of total 320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 30 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain G residue 82 VAL Chi-restraints excluded: chain A residue 45 LYS Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain C residue 43 LYS Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 50 HIS Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 82 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 4 optimal weight: 1.9990 chunk 17 optimal weight: 5.9990 chunk 24 optimal weight: 0.8980 chunk 36 optimal weight: 7.9990 chunk 38 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 10 optimal weight: 10.0000 chunk 32 optimal weight: 2.9990 chunk 21 optimal weight: 8.9990 chunk 0 optimal weight: 5.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 62 GLN C 50 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4077 moved from start: 0.9268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4168 Z= 0.140 Angle : 0.876 7.597 5864 Z= 0.354 Chirality : 0.052 0.138 568 Planarity : 0.004 0.033 592 Dihedral : 14.688 84.042 520 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 6.25 % Allowed : 24.38 % Favored : 69.38 % 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: -4.38 (0.30), residues: 448 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.33 (0.23), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.024 0.003 HIS C 50 PHE 0.008 0.001 PHE E 94 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 896 Ramachandran restraints generated. 448 Oldfield, 0 Emsley, 448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 896 Ramachandran restraints generated. 448 Oldfield, 0 Emsley, 448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 46 time to evaluate : 0.408 Fit side-chains revert: symmetry clash REVERT: E 45 LYS cc_start: 0.6891 (tttp) cc_final: 0.6593 (ttpt) REVERT: G 58 LYS cc_start: 0.6361 (mttt) cc_final: 0.5828 (mmmt) REVERT: C 46 GLU cc_start: 0.5493 (mt-10) cc_final: 0.5204 (mt-10) REVERT: C 97 LYS cc_start: 0.6915 (tttt) cc_final: 0.5850 (ttmt) outliers start: 20 outliers final: 15 residues processed: 63 average time/residue: 1.1292 time to fit residues: 73.7126 Evaluate side-chains 49 residues out of total 320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 34 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain G residue 82 VAL Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain C residue 43 LYS Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain D residue 82 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 28 optimal weight: 5.9990 chunk 15 optimal weight: 2.9990 chunk 32 optimal weight: 9.9990 chunk 26 optimal weight: 8.9990 chunk 0 optimal weight: 5.9990 chunk 19 optimal weight: 9.9990 chunk 34 optimal weight: 1.9990 chunk 9 optimal weight: 5.9990 chunk 13 optimal weight: 8.9990 chunk 7 optimal weight: 5.9990 chunk 22 optimal weight: 10.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4278 moved from start: 1.0031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 4168 Z= 0.270 Angle : 1.036 7.296 5864 Z= 0.452 Chirality : 0.057 0.149 568 Planarity : 0.005 0.021 592 Dihedral : 15.042 83.714 520 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 18.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.28 % Favored : 87.72 % Rotamer: Outliers : 9.69 % Allowed : 22.50 % Favored : 67.81 % 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: -4.41 (0.29), residues: 448 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.35 (0.22), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS H 50 PHE 0.016 0.003 PHE H 94 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 896 Ramachandran restraints generated. 448 Oldfield, 0 Emsley, 448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 896 Ramachandran restraints generated. 448 Oldfield, 0 Emsley, 448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 37 time to evaluate : 0.383 Fit side-chains revert: symmetry clash REVERT: G 58 LYS cc_start: 0.6850 (mttt) cc_final: 0.6628 (mmpt) REVERT: C 97 LYS cc_start: 0.7161 (tttt) cc_final: 0.5424 (pmtt) outliers start: 31 outliers final: 22 residues processed: 62 average time/residue: 0.8931 time to fit residues: 57.9782 Evaluate side-chains 53 residues out of total 320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 31 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 82 VAL Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain C residue 43 LYS Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 82 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 9 optimal weight: 4.9990 chunk 38 optimal weight: 0.9980 chunk 32 optimal weight: 5.9990 chunk 17 optimal weight: 7.9990 chunk 3 optimal weight: 3.9990 chunk 12 optimal weight: 4.9990 chunk 20 optimal weight: 10.0000 chunk 37 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 22 optimal weight: 9.9990 chunk 28 optimal weight: 0.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- 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: 0.4230 moved from start: 1.0252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 4168 Z= 0.159 Angle : 0.903 7.798 5864 Z= 0.377 Chirality : 0.053 0.194 568 Planarity : 0.003 0.015 592 Dihedral : 14.186 85.330 520 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 6.56 % Allowed : 25.62 % Favored : 67.81 % 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: -4.30 (0.29), residues: 448 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.27 (0.22), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 50 PHE 0.017 0.002 PHE A 94 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 896 Ramachandran restraints generated. 448 Oldfield, 0 Emsley, 448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 896 Ramachandran restraints generated. 448 Oldfield, 0 Emsley, 448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 43 time to evaluate : 0.346 Fit side-chains revert: symmetry clash REVERT: G 58 LYS cc_start: 0.6851 (mttt) cc_final: 0.6523 (mmpt) REVERT: C 46 GLU cc_start: 0.5981 (mt-10) cc_final: 0.5427 (mt-10) REVERT: C 87 SER cc_start: 0.7161 (t) cc_final: 0.6805 (m) REVERT: C 97 LYS cc_start: 0.7106 (tttt) cc_final: 0.5449 (pmtt) outliers start: 21 outliers final: 18 residues processed: 59 average time/residue: 0.9093 time to fit residues: 55.6906 Evaluate side-chains 53 residues out of total 320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 35 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain G residue 82 VAL Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain C residue 43 LYS Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain D residue 82 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 21 optimal weight: 6.9990 chunk 32 optimal weight: 9.9990 chunk 38 optimal weight: 10.0000 chunk 24 optimal weight: 0.0670 chunk 23 optimal weight: 5.9990 chunk 17 optimal weight: 10.0000 chunk 15 optimal weight: 0.7980 chunk 11 optimal weight: 6.9990 chunk 7 optimal weight: 3.9990 chunk 26 optimal weight: 5.9990 chunk 19 optimal weight: 6.9990 overall best weight: 3.3724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4309 moved from start: 1.0663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 4168 Z= 0.206 Angle : 0.949 7.468 5864 Z= 0.406 Chirality : 0.054 0.150 568 Planarity : 0.004 0.017 592 Dihedral : 14.024 87.517 520 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 15.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.50 % Favored : 87.50 % Rotamer: Outliers : 7.81 % Allowed : 25.00 % Favored : 67.19 % 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: -4.32 (0.29), residues: 448 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.29 (0.22), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS C 50 PHE 0.018 0.003 PHE H 94 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 896 Ramachandran restraints generated. 448 Oldfield, 0 Emsley, 448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 896 Ramachandran restraints generated. 448 Oldfield, 0 Emsley, 448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 39 time to evaluate : 0.376 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 58 LYS cc_start: 0.6853 (mttt) cc_final: 0.6520 (mmmt) REVERT: C 97 LYS cc_start: 0.7132 (tttt) cc_final: 0.5439 (pmtt) outliers start: 25 outliers final: 22 residues processed: 59 average time/residue: 0.8877 time to fit residues: 54.8537 Evaluate side-chains 56 residues out of total 320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 34 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain G residue 82 VAL Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 43 LYS Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 82 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 3 optimal weight: 9.9990 chunk 30 optimal weight: 10.0000 chunk 35 optimal weight: 8.9990 chunk 36 optimal weight: 9.9990 chunk 33 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 15 optimal weight: 10.0000 chunk 28 optimal weight: 0.0060 chunk 11 optimal weight: 0.0040 chunk 32 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 overall best weight: 1.2014 ------------------------------------------------------------------------------- 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: 0.4245 moved from start: 1.0784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4168 Z= 0.124 Angle : 0.847 7.605 5864 Z= 0.347 Chirality : 0.052 0.139 568 Planarity : 0.002 0.012 592 Dihedral : 13.534 88.995 520 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer: Outliers : 5.62 % Allowed : 27.81 % Favored : 66.56 % 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: -4.18 (0.30), residues: 448 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.18 (0.23), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 50 PHE 0.018 0.002 PHE H 94 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 896 Ramachandran restraints generated. 448 Oldfield, 0 Emsley, 448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 896 Ramachandran restraints generated. 448 Oldfield, 0 Emsley, 448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 46 time to evaluate : 0.358 Fit side-chains REVERT: H 83 GLU cc_start: 0.7576 (tp30) cc_final: 0.7246 (tp30) REVERT: B 58 LYS cc_start: 0.7312 (mttt) cc_final: 0.6625 (pptt) REVERT: C 46 GLU cc_start: 0.5954 (mt-10) cc_final: 0.5555 (mt-10) REVERT: C 87 SER cc_start: 0.7251 (t) cc_final: 0.6881 (m) REVERT: C 97 LYS cc_start: 0.6995 (tttt) cc_final: 0.5527 (pmmt) outliers start: 18 outliers final: 14 residues processed: 58 average time/residue: 0.9189 time to fit residues: 55.7276 Evaluate side-chains 54 residues out of total 320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 40 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain G residue 82 VAL Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain C residue 43 LYS Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain D residue 82 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 37 optimal weight: 10.0000 chunk 23 optimal weight: 4.9990 chunk 18 optimal weight: 10.0000 chunk 26 optimal weight: 0.8980 chunk 39 optimal weight: 8.9990 chunk 36 optimal weight: 10.0000 chunk 31 optimal weight: 4.9990 chunk 3 optimal weight: 0.0970 chunk 24 optimal weight: 0.9980 chunk 19 optimal weight: 8.9990 chunk 25 optimal weight: 5.9990 overall best weight: 2.3982 ------------------------------------------------------------------------------- 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: 0.4296 moved from start: 1.0974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 4168 Z= 0.167 Angle : 0.901 7.184 5864 Z= 0.380 Chirality : 0.053 0.141 568 Planarity : 0.003 0.014 592 Dihedral : 13.450 89.484 520 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.71 % Favored : 89.29 % Rotamer: Outliers : 5.94 % Allowed : 27.50 % Favored : 66.56 % 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: -4.16 (0.29), residues: 448 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.17 (0.22), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS C 50 PHE 0.015 0.002 PHE H 94 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 896 Ramachandran restraints generated. 448 Oldfield, 0 Emsley, 448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 896 Ramachandran restraints generated. 448 Oldfield, 0 Emsley, 448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 42 time to evaluate : 0.396 Fit side-chains revert: symmetry clash REVERT: B 58 LYS cc_start: 0.7378 (mttt) cc_final: 0.6722 (pptt) REVERT: C 46 GLU cc_start: 0.5944 (mt-10) cc_final: 0.5379 (mt-10) REVERT: C 97 LYS cc_start: 0.7031 (tttt) cc_final: 0.5357 (pmmt) outliers start: 19 outliers final: 17 residues processed: 55 average time/residue: 0.8662 time to fit residues: 49.9232 Evaluate side-chains 54 residues out of total 320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 37 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain G residue 82 VAL Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain H residue 54 THR Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain C residue 43 LYS Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain D residue 82 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 5.9990 chunk 9 optimal weight: 9.9990 chunk 29 optimal weight: 0.0040 chunk 4 optimal weight: 8.9990 chunk 8 optimal weight: 0.0070 chunk 31 optimal weight: 0.7980 chunk 13 optimal weight: 9.9990 chunk 32 optimal weight: 10.0000 chunk 5 optimal weight: 6.9990 chunk 27 optimal weight: 7.9990 chunk 1 optimal weight: 0.8980 overall best weight: 1.5412 ------------------------------------------------------------------------------- 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: 0.4274 moved from start: 1.1066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4168 Z= 0.136 Angle : 0.867 7.415 5864 Z= 0.361 Chirality : 0.052 0.133 568 Planarity : 0.003 0.015 592 Dihedral : 13.129 87.309 520 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 5.31 % Allowed : 28.44 % Favored : 66.25 % 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: -4.11 (0.30), residues: 448 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.12 (0.23), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 50 PHE 0.015 0.002 PHE H 94 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 896 Ramachandran restraints generated. 448 Oldfield, 0 Emsley, 448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 896 Ramachandran restraints generated. 448 Oldfield, 0 Emsley, 448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 43 time to evaluate : 0.396 Fit side-chains revert: symmetry clash REVERT: B 58 LYS cc_start: 0.7300 (mttt) cc_final: 0.6690 (pptt) REVERT: C 46 GLU cc_start: 0.5791 (mt-10) cc_final: 0.5461 (mt-10) REVERT: C 87 SER cc_start: 0.7255 (t) cc_final: 0.6845 (m) REVERT: C 97 LYS cc_start: 0.7008 (tttt) cc_final: 0.5616 (mptt) outliers start: 17 outliers final: 16 residues processed: 53 average time/residue: 0.7333 time to fit residues: 41.0771 Evaluate side-chains 55 residues out of total 320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 39 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain G residue 82 VAL Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain H residue 54 THR Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain C residue 43 LYS Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain D residue 82 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 22 optimal weight: 0.3980 chunk 36 optimal weight: 10.0000 chunk 21 optimal weight: 9.9990 chunk 27 optimal weight: 0.9990 chunk 1 optimal weight: 9.9990 chunk 25 optimal weight: 0.0670 chunk 24 optimal weight: 5.9990 chunk 23 optimal weight: 6.9990 chunk 15 optimal weight: 5.9990 chunk 14 optimal weight: 9.9990 chunk 39 optimal weight: 3.9990 overall best weight: 2.2924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5686 r_free = 0.5686 target = 0.296556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.5711 r_free = 0.5711 target = 0.271407 restraints weight = 7956.923| |-----------------------------------------------------------------------------| r_work (start): 0.5542 rms_B_bonded: 2.01 r_work: 0.5632 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.5554 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.5554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6085 moved from start: 1.1155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 4168 Z= 0.164 Angle : 0.890 7.312 5864 Z= 0.375 Chirality : 0.052 0.139 568 Planarity : 0.003 0.017 592 Dihedral : 13.127 84.699 520 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 13.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.49 % Favored : 89.51 % Rotamer: Outliers : 5.62 % Allowed : 27.50 % Favored : 66.88 % 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: -4.17 (0.29), residues: 448 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.17 (0.22), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 50 PHE 0.008 0.001 PHE F 94 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1773.19 seconds wall clock time: 32 minutes 33.18 seconds (1953.18 seconds total)