Starting phenix.real_space_refine on Mon Nov 13 18:41:52 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ynl_33965/11_2023/7ynl_33965_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ynl_33965/11_2023/7ynl_33965.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ynl_33965/11_2023/7ynl_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_33965/11_2023/7ynl_33965_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ynl_33965/11_2023/7ynl_33965_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ynl_33965/11_2023/7ynl_33965.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ynl_33965/11_2023/7ynl_33965.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ynl_33965/11_2023/7ynl_33965_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ynl_33965/11_2023/7ynl_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-1.21rc1-5144/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: 2.19, per 1000 atoms: 0.54 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: 1.74 Conformation dependent library (CDL) restraints added in 886.7 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: 0.62 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: 1.88 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: 2.200 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: 9.100 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 14.360 Find NCS groups from input model: 0.300 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:12.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.750 ------------------------------------------------------------------------------- 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 *********************** 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 : 0.336 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 1.0072 time to fit residues: 85.6477 Evaluate side-chains 30 residues out of total 320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 30 time to evaluate : 0.391 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4840 ------------------------------------------------------------------------------- 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: 0.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- 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: 0.3799 moved from start: 0.6578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 4168 Z= 0.263 Angle : 1.518 30.731 5864 Z= 0.564 Chirality : 0.054 0.166 568 Planarity : 0.009 0.058 592 Dihedral : 16.564 87.952 520 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 7.50 % Allowed : 15.00 % Favored : 77.50 % 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: -4.96 (0.27), residues: 448 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.77 (0.21), residues: 448 *********************** 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 73 residues out of total 320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 49 time to evaluate : 0.388 Fit side-chains outliers start: 24 outliers final: 11 residues processed: 68 average time/residue: 1.1102 time to fit residues: 78.2495 Evaluate side-chains 40 residues out of total 320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 29 time to evaluate : 0.372 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 10 residues processed: 1 average time/residue: 0.0371 time to fit residues: 0.5279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 10 optimal weight: 10.0000 chunk 36 optimal weight: 3.9990 chunk 39 optimal weight: 4.9990 chunk 32 optimal weight: 9.9990 chunk 12 optimal weight: 10.0000 chunk 29 optimal weight: 6.9990 chunk 35 optimal weight: 5.9990 chunk 27 optimal weight: 7.9990 chunk 18 optimal weight: 8.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- 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 C 50 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4153 moved from start: 0.9226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.063 4168 Z= 0.297 Angle : 1.232 28.597 5864 Z= 0.521 Chirality : 0.060 0.185 568 Planarity : 0.006 0.054 592 Dihedral : 16.074 88.710 520 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 15.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.16 % Favored : 88.84 % Rotamer: Outliers : 10.62 % Allowed : 20.31 % Favored : 69.06 % 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: -4.72 (0.29), residues: 448 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.59 (0.22), residues: 448 *********************** 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 78 residues out of total 320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 44 time to evaluate : 0.388 Fit side-chains revert: symmetry clash outliers start: 34 outliers final: 21 residues processed: 71 average time/residue: 1.0900 time to fit residues: 80.3063 Evaluate side-chains 55 residues out of total 320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 34 time to evaluate : 0.364 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 19 residues processed: 2 average time/residue: 0.0395 time to fit residues: 0.6289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 4 optimal weight: 0.9980 chunk 17 optimal weight: 6.9990 chunk 24 optimal weight: 0.9990 chunk 36 optimal weight: 0.7980 chunk 38 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 chunk 34 optimal weight: 5.9990 chunk 10 optimal weight: 7.9990 chunk 32 optimal weight: 5.9990 chunk 21 optimal weight: 10.0000 chunk 0 optimal weight: 8.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 62 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4082 moved from start: 0.9536 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= 0.138 Angle : 0.874 7.516 5864 Z= 0.359 Chirality : 0.053 0.134 568 Planarity : 0.003 0.014 592 Dihedral : 14.768 85.535 520 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 9.69 % Allowed : 22.81 % Favored : 67.50 % 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: -4.42 (0.29), residues: 448 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.36 (0.22), residues: 448 *********************** 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 75 residues out of total 320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 44 time to evaluate : 0.409 Fit side-chains revert: symmetry clash outliers start: 31 outliers final: 24 residues processed: 71 average time/residue: 1.0827 time to fit residues: 79.7364 Evaluate side-chains 55 residues out of total 320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 31 time to evaluate : 0.400 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 21 residues processed: 3 average time/residue: 0.0396 time to fit residues: 0.7146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 28 optimal weight: 2.9990 chunk 15 optimal weight: 9.9990 chunk 32 optimal weight: 9.9990 chunk 26 optimal weight: 9.9990 chunk 0 optimal weight: 9.9990 chunk 19 optimal weight: 6.9990 chunk 34 optimal weight: 7.9990 chunk 9 optimal weight: 0.3980 chunk 13 optimal weight: 1.9990 chunk 7 optimal weight: 9.9990 chunk 22 optimal weight: 10.0000 overall best weight: 4.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 50 HIS ** D 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4250 moved from start: 1.0231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 4168 Z= 0.244 Angle : 1.003 7.661 5864 Z= 0.434 Chirality : 0.057 0.157 568 Planarity : 0.004 0.019 592 Dihedral : 14.809 89.651 520 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 16.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.05 % Favored : 87.95 % Rotamer: Outliers : 10.94 % Allowed : 24.38 % Favored : 64.69 % 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: -4.43 (0.29), residues: 448 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.37 (0.22), residues: 448 *********************** 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 71 residues out of total 320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 36 time to evaluate : 0.413 Fit side-chains outliers start: 35 outliers final: 26 residues processed: 65 average time/residue: 0.9050 time to fit residues: 61.5025 Evaluate side-chains 54 residues out of total 320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 28 time to evaluate : 0.393 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 22 residues processed: 4 average time/residue: 0.0395 time to fit residues: 0.7438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 9 optimal weight: 0.0070 chunk 38 optimal weight: 1.9990 chunk 32 optimal weight: 5.9990 chunk 17 optimal weight: 10.0000 chunk 3 optimal weight: 5.9990 chunk 12 optimal weight: 2.9990 chunk 20 optimal weight: 10.0000 chunk 37 optimal weight: 3.9990 chunk 4 optimal weight: 7.9990 chunk 22 optimal weight: 1.9990 chunk 28 optimal weight: 5.9990 overall best weight: 2.2006 ------------------------------------------------------------------------------- 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: 0.4211 moved from start: 1.0462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 4168 Z= 0.155 Angle : 0.887 8.552 5864 Z= 0.370 Chirality : 0.053 0.134 568 Planarity : 0.003 0.014 592 Dihedral : 13.938 80.755 520 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 8.75 % Allowed : 25.00 % 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: -4.35 (0.29), residues: 448 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.31 (0.22), residues: 448 *********************** 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 69 residues out of total 320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 41 time to evaluate : 0.276 Fit side-chains revert: symmetry clash outliers start: 28 outliers final: 24 residues processed: 65 average time/residue: 0.5430 time to fit residues: 37.0870 Evaluate side-chains 55 residues out of total 320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 31 time to evaluate : 0.284 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 21 residues processed: 3 average time/residue: 0.0310 time to fit residues: 0.5134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 21 optimal weight: 9.9990 chunk 32 optimal weight: 10.0000 chunk 38 optimal weight: 10.0000 chunk 24 optimal weight: 9.9990 chunk 23 optimal weight: 2.9990 chunk 17 optimal weight: 9.9990 chunk 15 optimal weight: 10.0000 chunk 11 optimal weight: 7.9990 chunk 7 optimal weight: 9.9990 chunk 26 optimal weight: 3.9990 chunk 19 optimal weight: 7.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 50 HIS ** D 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4378 moved from start: 1.1056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.056 4168 Z= 0.341 Angle : 1.150 7.884 5864 Z= 0.515 Chirality : 0.063 0.192 568 Planarity : 0.005 0.025 592 Dihedral : 14.532 80.666 520 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 18.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.40 % Favored : 84.60 % Rotamer: Outliers : 11.88 % Allowed : 21.56 % 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: -4.36 (0.29), residues: 448 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.31 (0.22), residues: 448 *********************** 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 71 residues out of total 320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 33 time to evaluate : 0.388 Fit side-chains revert: symmetry clash outliers start: 38 outliers final: 30 residues processed: 65 average time/residue: 0.9109 time to fit residues: 61.8247 Evaluate side-chains 57 residues out of total 320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 27 time to evaluate : 0.392 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 27 residues processed: 3 average time/residue: 0.0396 time to fit residues: 0.7054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 3 optimal weight: 7.9990 chunk 30 optimal weight: 6.9990 chunk 35 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 chunk 33 optimal weight: 0.7980 chunk 21 optimal weight: 8.9990 chunk 15 optimal weight: 4.9990 chunk 28 optimal weight: 7.9990 chunk 11 optimal weight: 2.9990 chunk 32 optimal weight: 10.0000 chunk 23 optimal weight: 6.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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: 0.4331 moved from start: 1.1198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 4168 Z= 0.210 Angle : 0.985 9.001 5864 Z= 0.426 Chirality : 0.056 0.147 568 Planarity : 0.004 0.018 592 Dihedral : 13.791 79.804 520 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 15.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.82 % Favored : 90.18 % Rotamer: Outliers : 9.38 % Allowed : 24.38 % 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: -4.36 (0.29), residues: 448 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.31 (0.22), residues: 448 *********************** 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 66 residues out of total 320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 36 time to evaluate : 0.390 Fit side-chains revert: symmetry clash outliers start: 30 outliers final: 29 residues processed: 65 average time/residue: 0.7862 time to fit residues: 53.7645 Evaluate side-chains 61 residues out of total 320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 32 time to evaluate : 0.390 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 28 residues processed: 1 average time/residue: 0.0375 time to fit residues: 0.5750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 37 optimal weight: 9.9990 chunk 23 optimal weight: 0.8980 chunk 18 optimal weight: 9.9990 chunk 26 optimal weight: 5.9990 chunk 39 optimal weight: 3.9990 chunk 36 optimal weight: 0.8980 chunk 31 optimal weight: 3.9990 chunk 3 optimal weight: 5.9990 chunk 24 optimal weight: 4.9990 chunk 19 optimal weight: 5.9990 chunk 25 optimal weight: 0.8980 overall best weight: 2.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4301 moved from start: 1.1310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 4168 Z= 0.156 Angle : 0.902 8.773 5864 Z= 0.379 Chirality : 0.053 0.139 568 Planarity : 0.003 0.014 592 Dihedral : 13.137 78.377 520 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.49 % Favored : 89.51 % Rotamer: Outliers : 9.38 % Allowed : 23.75 % 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: -4.33 (0.29), residues: 448 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.29 (0.22), residues: 448 *********************** 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 74 residues out of total 320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 44 time to evaluate : 0.415 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 28 residues processed: 72 average time/residue: 0.7238 time to fit residues: 54.8885 Evaluate side-chains 66 residues out of total 320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 38 time to evaluate : 0.404 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 26 residues processed: 2 average time/residue: 0.0404 time to fit residues: 0.6322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 0.0010 chunk 9 optimal weight: 7.9990 chunk 29 optimal weight: 3.9990 chunk 4 optimal weight: 8.9990 chunk 8 optimal weight: 0.9990 chunk 31 optimal weight: 6.9990 chunk 13 optimal weight: 0.1980 chunk 32 optimal weight: 6.9990 chunk 5 optimal weight: 1.9990 chunk 27 optimal weight: 10.0000 chunk 1 optimal weight: 3.9990 overall best weight: 1.4392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 79 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4283 moved from start: 1.1409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4168 Z= 0.139 Angle : 0.881 8.253 5864 Z= 0.369 Chirality : 0.052 0.139 568 Planarity : 0.002 0.013 592 Dihedral : 12.788 77.086 520 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 9.06 % Allowed : 24.38 % 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: -4.26 (0.29), residues: 448 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.24 (0.22), residues: 448 ********************** 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 70 residues out of total 320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 41 time to evaluate : 0.389 Fit side-chains revert: symmetry clash outliers start: 29 outliers final: 26 residues processed: 69 average time/residue: 0.6959 time to fit residues: 50.8237 Evaluate side-chains 62 residues out of total 320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 36 time to evaluate : 0.397 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 25 residues processed: 1 average time/residue: 0.0396 time to fit residues: 0.5482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 22 optimal weight: 10.0000 chunk 36 optimal weight: 9.9990 chunk 21 optimal weight: 9.9990 chunk 27 optimal weight: 0.9980 chunk 1 optimal weight: 4.9990 chunk 25 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 23 optimal weight: 7.9990 chunk 15 optimal weight: 10.0000 chunk 14 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5706 r_free = 0.5706 target = 0.300711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.5728 r_free = 0.5728 target = 0.273771 restraints weight = 7860.988| |-----------------------------------------------------------------------------| r_work (start): 0.5520 rms_B_bonded: 1.92 r_work: 0.5381 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.5381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6170 moved from start: 1.1510 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= 0.149 Angle : 0.891 8.060 5864 Z= 0.376 Chirality : 0.053 0.137 568 Planarity : 0.003 0.015 592 Dihedral : 12.772 76.554 520 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.60 % Favored : 90.40 % Rotamer: Outliers : 8.44 % Allowed : 25.31 % 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: -4.15 (0.29), residues: 448 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.16 (0.22), residues: 448 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1756.20 seconds wall clock time: 34 minutes 11.54 seconds (2051.54 seconds total)