Starting phenix.real_space_refine on Wed Nov 13 22:53:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ihv_35460/11_2024/8ihv_35460.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ihv_35460/11_2024/8ihv_35460.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.11 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ihv_35460/11_2024/8ihv_35460.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ihv_35460/11_2024/8ihv_35460.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ihv_35460/11_2024/8ihv_35460.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ihv_35460/11_2024/8ihv_35460.cif" } resolution = 3.11 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= 0.000 sd= 0.001 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 6 5.16 5 C 864 2.51 5 N 261 2.21 5 O 315 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 1446 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 482 Classifications: {'peptide': 69} Link IDs: {'TRANS': 68} Restraints were copied for chains: C, B Time building chain proxies: 1.33, per 1000 atoms: 0.92 Number of scatterers: 1446 At special positions: 0 Unit cell: (78.12, 63, 37.8, 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 6 16.00 O 315 8.00 N 261 7.00 C 864 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.09 Conformation dependent library (CDL) restraints added in 204.4 milliseconds 402 Ramachandran restraints generated. 201 Oldfield, 0 Emsley, 201 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 348 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 5 sheets defined 0.0% alpha, 13.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 97 through 99 Processing sheet with id=AA2, first strand: chain 'A' and resid 103 through 105 Processing sheet with id=AA3, first strand: chain 'A' and resid 112 through 113 Processing sheet with id=AA4, first strand: chain 'A' and resid 117 through 120 Processing sheet with id=AA5, first strand: chain 'A' and resid 123 through 125 removed outlier: 6.951A pdb=" N ASP B 124 " --> pdb=" O ALA A 123 " (cutoff:3.500A) 17 hydrogen bonds defined for protein. 51 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.28 Time building geometry restraints manager: 2.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 531 1.34 - 1.45: 99 1.45 - 1.57: 813 1.57 - 1.68: 0 1.68 - 1.80: 6 Bond restraints: 1449 Sorted by residual: bond pdb=" CB ASN C 139 " pdb=" CG ASN C 139 " ideal model delta sigma weight residual 1.516 1.487 0.029 2.50e-02 1.60e+03 1.32e+00 bond pdb=" CB ASN A 139 " pdb=" CG ASN A 139 " ideal model delta sigma weight residual 1.516 1.487 0.029 2.50e-02 1.60e+03 1.31e+00 bond pdb=" CB ASN B 139 " pdb=" CG ASN B 139 " ideal model delta sigma weight residual 1.516 1.487 0.029 2.50e-02 1.60e+03 1.30e+00 bond pdb=" C ASP C 101 " pdb=" N SER C 102 " ideal model delta sigma weight residual 1.328 1.319 0.010 1.23e-02 6.61e+03 6.21e-01 bond pdb=" CA ASP C 124 " pdb=" CB ASP C 124 " ideal model delta sigma weight residual 1.537 1.523 0.014 1.76e-02 3.23e+03 6.20e-01 ... (remaining 1444 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.18: 1798 1.18 - 2.37: 118 2.37 - 3.55: 24 3.55 - 4.73: 7 4.73 - 5.91: 3 Bond angle restraints: 1950 Sorted by residual: angle pdb=" N ILE A 149 " pdb=" CA ILE A 149 " pdb=" C ILE A 149 " ideal model delta sigma weight residual 109.34 115.25 -5.91 2.08e+00 2.31e-01 8.08e+00 angle pdb=" N ILE C 149 " pdb=" CA ILE C 149 " pdb=" C ILE C 149 " ideal model delta sigma weight residual 109.34 115.22 -5.88 2.08e+00 2.31e-01 7.99e+00 angle pdb=" N ILE B 149 " pdb=" CA ILE B 149 " pdb=" C ILE B 149 " ideal model delta sigma weight residual 109.34 115.21 -5.87 2.08e+00 2.31e-01 7.98e+00 angle pdb=" C ALA B 123 " pdb=" N ASP B 124 " pdb=" CA ASP B 124 " ideal model delta sigma weight residual 122.46 118.89 3.57 1.80e+00 3.09e-01 3.93e+00 angle pdb=" C VAL B 148 " pdb=" N ILE B 149 " pdb=" CA ILE B 149 " ideal model delta sigma weight residual 121.97 125.51 -3.54 1.80e+00 3.09e-01 3.87e+00 ... (remaining 1945 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 8.47: 651 8.47 - 16.94: 117 16.94 - 25.41: 67 25.41 - 33.88: 14 33.88 - 42.35: 15 Dihedral angle restraints: 864 sinusoidal: 312 harmonic: 552 Sorted by residual: dihedral pdb=" CA GLU B 100 " pdb=" C GLU B 100 " pdb=" N ASP B 101 " pdb=" CA ASP B 101 " ideal model delta harmonic sigma weight residual -180.00 -162.32 -17.68 0 5.00e+00 4.00e-02 1.25e+01 dihedral pdb=" CA GLU A 100 " pdb=" C GLU A 100 " pdb=" N ASP A 101 " pdb=" CA ASP A 101 " ideal model delta harmonic sigma weight residual -180.00 -162.33 -17.67 0 5.00e+00 4.00e-02 1.25e+01 dihedral pdb=" CA GLU C 100 " pdb=" C GLU C 100 " pdb=" N ASP C 101 " pdb=" CA ASP C 101 " ideal model delta harmonic sigma weight residual -180.00 -162.39 -17.61 0 5.00e+00 4.00e-02 1.24e+01 ... (remaining 861 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 127 0.031 - 0.061: 74 0.061 - 0.091: 15 0.091 - 0.122: 16 0.122 - 0.152: 5 Chirality restraints: 237 Sorted by residual: chirality pdb=" CB ILE C 112 " pdb=" CA ILE C 112 " pdb=" CG1 ILE C 112 " pdb=" CG2 ILE C 112 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.15 2.00e-01 2.50e+01 5.81e-01 chirality pdb=" CB ILE B 112 " pdb=" CA ILE B 112 " pdb=" CG1 ILE B 112 " pdb=" CG2 ILE B 112 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.15 2.00e-01 2.50e+01 5.65e-01 chirality pdb=" CB ILE A 112 " pdb=" CA ILE A 112 " pdb=" CG1 ILE A 112 " pdb=" CG2 ILE A 112 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.15 2.00e-01 2.50e+01 5.57e-01 ... (remaining 234 not shown) Planarity restraints: 261 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP B 101 " 0.006 2.00e-02 2.50e+03 1.22e-02 1.50e+00 pdb=" C ASP B 101 " -0.021 2.00e-02 2.50e+03 pdb=" O ASP B 101 " 0.008 2.00e-02 2.50e+03 pdb=" N SER B 102 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP C 101 " 0.006 2.00e-02 2.50e+03 1.21e-02 1.47e+00 pdb=" C ASP C 101 " -0.021 2.00e-02 2.50e+03 pdb=" O ASP C 101 " 0.008 2.00e-02 2.50e+03 pdb=" N SER C 102 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 101 " 0.006 2.00e-02 2.50e+03 1.20e-02 1.45e+00 pdb=" C ASP A 101 " -0.021 2.00e-02 2.50e+03 pdb=" O ASP A 101 " 0.008 2.00e-02 2.50e+03 pdb=" N SER A 102 " 0.007 2.00e-02 2.50e+03 ... (remaining 258 not shown) Histogram of nonbonded interaction distances: 2.39 - 2.90: 643 2.90 - 3.40: 1286 3.40 - 3.90: 2048 3.90 - 4.40: 2290 4.40 - 4.90: 4494 Nonbonded interactions: 10761 Sorted by model distance: nonbonded pdb=" OD1 ASP C 92 " pdb=" N GLY C 93 " model vdw 2.395 3.120 nonbonded pdb=" OD1 ASP A 92 " pdb=" N GLY A 93 " model vdw 2.395 3.120 nonbonded pdb=" OD1 ASP B 92 " pdb=" N GLY B 93 " model vdw 2.395 3.120 nonbonded pdb=" OG SER B 134 " pdb=" NH2 ARG C 143 " model vdw 2.455 3.120 nonbonded pdb=" N ASP C 101 " pdb=" OD1 ASP C 101 " model vdw 2.462 3.120 ... (remaining 10756 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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: 2.720 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: 0.010 Extract box with map and model: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 10.830 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 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 : 0.005 0.029 1449 Z= 0.391 Angle : 0.729 5.914 1950 Z= 0.409 Chirality : 0.048 0.152 237 Planarity : 0.002 0.012 261 Dihedral : 13.404 42.355 516 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 23.88 % Favored : 76.12 % Rotamer: Outliers : 0.00 % Allowed : 15.38 % Favored : 84.62 % 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: -6.37 (0.35), residues: 201 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.85 (0.26), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.002 HIS B 120 ARG 0.001 0.000 ARG A 115 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 402 Ramachandran restraints generated. 201 Oldfield, 0 Emsley, 201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 402 Ramachandran restraints generated. 201 Oldfield, 0 Emsley, 201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 0.167 Fit side-chains revert: symmetry clash REVERT: A 101 ASP cc_start: 0.8306 (p0) cc_final: 0.8079 (p0) REVERT: B 101 ASP cc_start: 0.8203 (p0) cc_final: 0.7857 (p0) REVERT: B 128 LYS cc_start: 0.7774 (mmmt) cc_final: 0.7354 (mmtm) REVERT: B 131 ASN cc_start: 0.8264 (t0) cc_final: 0.8061 (t0) REVERT: C 92 ASP cc_start: 0.7944 (t0) cc_final: 0.7717 (t0) REVERT: C 128 LYS cc_start: 0.7647 (mmmt) cc_final: 0.7267 (tptt) REVERT: C 131 ASN cc_start: 0.8702 (t0) cc_final: 0.8306 (t0) outliers start: 0 outliers final: 0 residues processed: 36 average time/residue: 0.1987 time to fit residues: 7.8775 Evaluate side-chains 32 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 15 optimal weight: 3.9990 chunk 13 optimal weight: 0.8980 chunk 7 optimal weight: 0.9990 chunk 4 optimal weight: 5.9990 chunk 9 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 16 optimal weight: 0.8980 chunk 11 optimal weight: 0.5980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 139 ASN B 139 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.1464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 1449 Z= 0.186 Angle : 0.618 6.680 1950 Z= 0.321 Chirality : 0.047 0.123 237 Planarity : 0.002 0.008 261 Dihedral : 4.625 16.814 210 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.42 % Favored : 84.58 % Rotamer: Outliers : 3.85 % Allowed : 16.67 % Favored : 79.49 % 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: -5.51 (0.42), residues: 201 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.20 (0.32), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 110 ARG 0.001 0.000 ARG C 143 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 402 Ramachandran restraints generated. 201 Oldfield, 0 Emsley, 201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 402 Ramachandran restraints generated. 201 Oldfield, 0 Emsley, 201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 28 time to evaluate : 0.156 Fit side-chains revert: symmetry clash REVERT: A 112 ILE cc_start: 0.8647 (OUTLIER) cc_final: 0.8140 (mt) REVERT: A 143 ARG cc_start: 0.8372 (ttt180) cc_final: 0.6263 (mtm180) REVERT: B 112 ILE cc_start: 0.8126 (OUTLIER) cc_final: 0.7703 (mt) REVERT: B 128 LYS cc_start: 0.7774 (mmmt) cc_final: 0.7347 (mmtp) REVERT: B 131 ASN cc_start: 0.8148 (t0) cc_final: 0.7889 (t0) REVERT: C 112 ILE cc_start: 0.7806 (OUTLIER) cc_final: 0.7505 (mt) REVERT: C 128 LYS cc_start: 0.7757 (mmmt) cc_final: 0.7371 (tptt) REVERT: C 131 ASN cc_start: 0.8668 (t0) cc_final: 0.8253 (t0) outliers start: 6 outliers final: 2 residues processed: 30 average time/residue: 0.1941 time to fit residues: 6.3875 Evaluate side-chains 29 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 24 time to evaluate : 0.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain C residue 112 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 4 optimal weight: 7.9990 chunk 16 optimal weight: 0.0040 chunk 17 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 5 optimal weight: 0.0000 chunk 13 optimal weight: 5.9990 chunk 12 optimal weight: 9.9990 chunk 8 optimal weight: 0.8980 chunk 1 optimal weight: 6.9990 chunk 7 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 overall best weight: 0.7398 ------------------------------------------------------------------------------- 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: 0.8015 moved from start: 0.1878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.014 1449 Z= 0.160 Angle : 0.571 6.845 1950 Z= 0.297 Chirality : 0.046 0.119 237 Planarity : 0.002 0.011 261 Dihedral : 4.183 15.763 210 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.41 % Favored : 82.59 % Rotamer: Outliers : 6.41 % Allowed : 13.46 % Favored : 80.13 % 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: -5.10 (0.47), residues: 201 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.88 (0.36), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 110 ARG 0.001 0.000 ARG B 143 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 402 Ramachandran restraints generated. 201 Oldfield, 0 Emsley, 201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 402 Ramachandran restraints generated. 201 Oldfield, 0 Emsley, 201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 22 time to evaluate : 0.165 Fit side-chains revert: symmetry clash REVERT: A 143 ARG cc_start: 0.8380 (ttt180) cc_final: 0.6267 (mtm180) REVERT: B 128 LYS cc_start: 0.7783 (mmmt) cc_final: 0.7310 (mmtm) REVERT: B 131 ASN cc_start: 0.8088 (t0) cc_final: 0.7826 (t0) REVERT: B 133 GLU cc_start: 0.7924 (mm-30) cc_final: 0.7690 (mm-30) REVERT: C 92 ASP cc_start: 0.7796 (t0) cc_final: 0.7585 (t0) REVERT: C 128 LYS cc_start: 0.7720 (mmmt) cc_final: 0.7359 (tptt) outliers start: 10 outliers final: 4 residues processed: 27 average time/residue: 0.1862 time to fit residues: 5.6160 Evaluate side-chains 25 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 21 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain C residue 112 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 16 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 8 optimal weight: 5.9990 chunk 15 optimal weight: 3.9990 chunk 4 optimal weight: 6.9990 chunk 14 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 12 optimal weight: 10.0000 chunk 7 optimal weight: 0.9980 chunk 5 optimal weight: 4.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- 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: 0.8123 moved from start: 0.1773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.036 1449 Z= 0.435 Angle : 0.714 6.622 1950 Z= 0.395 Chirality : 0.051 0.128 237 Planarity : 0.003 0.012 261 Dihedral : 5.349 17.399 210 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 21.39 % Favored : 78.61 % Rotamer: Outliers : 4.49 % Allowed : 14.74 % Favored : 80.77 % 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: -5.32 (0.45), residues: 201 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.05 (0.35), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS A 120 ARG 0.001 0.000 ARG A 143 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 402 Ramachandran restraints generated. 201 Oldfield, 0 Emsley, 201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 402 Ramachandran restraints generated. 201 Oldfield, 0 Emsley, 201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 22 time to evaluate : 0.190 Fit side-chains revert: symmetry clash REVERT: B 128 LYS cc_start: 0.7869 (mmmt) cc_final: 0.7417 (mmtm) REVERT: B 131 ASN cc_start: 0.8206 (t0) cc_final: 0.7992 (t0) REVERT: B 133 GLU cc_start: 0.8012 (mm-30) cc_final: 0.7773 (mm-30) REVERT: C 128 LYS cc_start: 0.7736 (mmmt) cc_final: 0.7375 (tptt) REVERT: C 131 ASN cc_start: 0.8752 (t0) cc_final: 0.8373 (t0) outliers start: 7 outliers final: 6 residues processed: 23 average time/residue: 0.1751 time to fit residues: 4.5952 Evaluate side-chains 28 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 22 time to evaluate : 0.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 112 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 15 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 10 optimal weight: 5.9990 chunk 4 optimal weight: 0.7980 chunk 17 optimal weight: 0.9990 chunk 14 optimal weight: 3.9990 chunk 8 optimal weight: 0.9990 chunk 1 optimal weight: 0.1980 chunk 5 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 overall best weight: 0.7984 ------------------------------------------------------------------------------- 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: 0.8026 moved from start: 0.2134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 1449 Z= 0.169 Angle : 0.579 7.070 1950 Z= 0.304 Chirality : 0.047 0.118 237 Planarity : 0.002 0.012 261 Dihedral : 4.251 15.735 210 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.42 % Favored : 83.58 % Rotamer: Outliers : 3.85 % Allowed : 16.03 % Favored : 80.13 % 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 (0.48), residues: 201 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.78 (0.37), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 110 ARG 0.001 0.000 ARG A 115 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 402 Ramachandran restraints generated. 201 Oldfield, 0 Emsley, 201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 402 Ramachandran restraints generated. 201 Oldfield, 0 Emsley, 201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 21 time to evaluate : 0.166 Fit side-chains revert: symmetry clash REVERT: A 112 ILE cc_start: 0.8570 (OUTLIER) cc_final: 0.8012 (mt) REVERT: A 143 ARG cc_start: 0.8331 (ttt180) cc_final: 0.6220 (mtm180) REVERT: B 128 LYS cc_start: 0.7850 (mmmt) cc_final: 0.7427 (mmtm) REVERT: B 133 GLU cc_start: 0.7905 (mm-30) cc_final: 0.7688 (mm-30) REVERT: C 128 LYS cc_start: 0.7710 (mmmt) cc_final: 0.7365 (tptt) outliers start: 6 outliers final: 4 residues processed: 21 average time/residue: 0.2656 time to fit residues: 6.0922 Evaluate side-chains 24 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 19 time to evaluate : 0.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain C residue 112 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 1 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 12 optimal weight: 3.9990 chunk 14 optimal weight: 4.9990 chunk 17 optimal weight: 0.5980 chunk 10 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 3 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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: 0.8055 moved from start: 0.2029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 1449 Z= 0.246 Angle : 0.619 9.300 1950 Z= 0.325 Chirality : 0.047 0.116 237 Planarity : 0.002 0.017 261 Dihedral : 4.466 15.500 210 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 19.40 % Favored : 80.60 % Rotamer: Outliers : 3.85 % Allowed : 17.95 % Favored : 78.21 % 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: -4.95 (0.49), residues: 201 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.76 (0.37), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 110 ARG 0.003 0.000 ARG B 143 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 402 Ramachandran restraints generated. 201 Oldfield, 0 Emsley, 201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 402 Ramachandran restraints generated. 201 Oldfield, 0 Emsley, 201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 22 time to evaluate : 0.167 Fit side-chains revert: symmetry clash REVERT: A 143 ARG cc_start: 0.8413 (ttt180) cc_final: 0.6253 (mtm180) REVERT: B 128 LYS cc_start: 0.7919 (mmmt) cc_final: 0.7470 (mmtm) REVERT: B 131 ASN cc_start: 0.8090 (t0) cc_final: 0.7835 (t0) REVERT: C 128 LYS cc_start: 0.7719 (mmmt) cc_final: 0.7348 (tptt) REVERT: C 131 ASN cc_start: 0.8706 (t0) cc_final: 0.8294 (t0) outliers start: 6 outliers final: 4 residues processed: 22 average time/residue: 0.2216 time to fit residues: 5.4041 Evaluate side-chains 26 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 22 time to evaluate : 0.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain C residue 112 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 11 optimal weight: 3.9990 chunk 8 optimal weight: 5.9990 chunk 1 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 16 optimal weight: 5.9990 chunk 9 optimal weight: 0.8980 chunk 7 optimal weight: 0.8980 chunk 12 optimal weight: 7.9990 chunk 4 optimal weight: 5.9990 chunk 14 optimal weight: 0.5980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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: 0.8011 moved from start: 0.2315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 1449 Z= 0.167 Angle : 0.553 7.372 1950 Z= 0.296 Chirality : 0.046 0.114 237 Planarity : 0.002 0.014 261 Dihedral : 4.025 15.065 210 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.92 % Favored : 84.08 % Rotamer: Outliers : 3.21 % Allowed : 19.87 % Favored : 76.92 % 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: -4.85 (0.49), residues: 201 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.69 (0.37), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 110 ARG 0.002 0.000 ARG B 143 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 402 Ramachandran restraints generated. 201 Oldfield, 0 Emsley, 201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 402 Ramachandran restraints generated. 201 Oldfield, 0 Emsley, 201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 20 time to evaluate : 0.165 Fit side-chains revert: symmetry clash REVERT: A 143 ARG cc_start: 0.8392 (ttt180) cc_final: 0.6269 (mtm180) REVERT: B 128 LYS cc_start: 0.7883 (mmmt) cc_final: 0.7459 (mmtm) REVERT: B 131 ASN cc_start: 0.8071 (t0) cc_final: 0.7827 (t0) REVERT: C 128 LYS cc_start: 0.7726 (mmmt) cc_final: 0.7380 (tptt) outliers start: 5 outliers final: 4 residues processed: 21 average time/residue: 0.2200 time to fit residues: 5.1324 Evaluate side-chains 24 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 20 time to evaluate : 0.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain C residue 112 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 15 optimal weight: 1.9990 chunk 16 optimal weight: 5.9990 chunk 10 optimal weight: 7.9990 chunk 17 optimal weight: 4.9990 chunk 8 optimal weight: 5.9990 chunk 11 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- 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: 0.8066 moved from start: 0.2121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 1449 Z= 0.285 Angle : 0.621 6.762 1950 Z= 0.338 Chirality : 0.047 0.116 237 Planarity : 0.002 0.010 261 Dihedral : 4.531 15.582 210 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 1.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 19.90 % Favored : 80.10 % Rotamer: Outliers : 2.56 % Allowed : 20.51 % Favored : 76.92 % 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: -4.90 (0.49), residues: 201 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.73 (0.37), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 110 ARG 0.001 0.000 ARG B 143 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 402 Ramachandran restraints generated. 201 Oldfield, 0 Emsley, 201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 402 Ramachandran restraints generated. 201 Oldfield, 0 Emsley, 201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 21 time to evaluate : 0.173 Fit side-chains revert: symmetry clash REVERT: B 128 LYS cc_start: 0.7849 (mmmt) cc_final: 0.7415 (mmtm) REVERT: B 131 ASN cc_start: 0.8108 (t0) cc_final: 0.7869 (t0) REVERT: C 128 LYS cc_start: 0.7690 (mmmt) cc_final: 0.7332 (tptt) REVERT: C 131 ASN cc_start: 0.8711 (t0) cc_final: 0.8307 (t0) outliers start: 4 outliers final: 4 residues processed: 21 average time/residue: 0.2272 time to fit residues: 5.2897 Evaluate side-chains 24 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 20 time to evaluate : 0.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain C residue 112 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 3 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 chunk 5 optimal weight: 0.6980 chunk 1 optimal weight: 4.9990 chunk 2 optimal weight: 5.9990 chunk 12 optimal weight: 0.0040 chunk 0 optimal weight: 10.0000 chunk 10 optimal weight: 8.9990 chunk 16 optimal weight: 0.8980 chunk 9 optimal weight: 0.6980 chunk 11 optimal weight: 0.9990 overall best weight: 0.6594 ------------------------------------------------------------------------------- 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: 0.7991 moved from start: 0.2451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 1449 Z= 0.149 Angle : 0.568 5.818 1950 Z= 0.310 Chirality : 0.046 0.113 237 Planarity : 0.002 0.011 261 Dihedral : 3.838 15.114 210 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.43 % Favored : 85.57 % Rotamer: Outliers : 2.56 % Allowed : 20.51 % Favored : 76.92 % 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: -4.73 (0.50), residues: 201 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.59 (0.38), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 110 ARG 0.001 0.000 ARG B 143 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 402 Ramachandran restraints generated. 201 Oldfield, 0 Emsley, 201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 402 Ramachandran restraints generated. 201 Oldfield, 0 Emsley, 201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 18 time to evaluate : 0.167 Fit side-chains revert: symmetry clash REVERT: B 128 LYS cc_start: 0.7795 (mmmt) cc_final: 0.7402 (mmtm) REVERT: C 128 LYS cc_start: 0.7725 (mmmt) cc_final: 0.7380 (tptt) outliers start: 4 outliers final: 4 residues processed: 18 average time/residue: 0.2361 time to fit residues: 4.7395 Evaluate side-chains 22 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 18 time to evaluate : 0.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain C residue 112 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 10 optimal weight: 7.9990 chunk 7 optimal weight: 3.9990 chunk 6 optimal weight: 0.9990 chunk 17 optimal weight: 4.9990 chunk 0 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 2 optimal weight: 5.9990 chunk 14 optimal weight: 0.9990 chunk 16 optimal weight: 0.5980 chunk 1 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- 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: 0.8071 moved from start: 0.2155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 1449 Z= 0.308 Angle : 0.643 5.770 1950 Z= 0.354 Chirality : 0.048 0.118 237 Planarity : 0.002 0.008 261 Dihedral : 4.559 15.559 210 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 19.40 % Favored : 80.60 % Rotamer: Outliers : 3.85 % Allowed : 19.23 % Favored : 76.92 % 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: -4.84 (0.50), residues: 201 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.68 (0.38), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 120 ARG 0.002 0.000 ARG B 143 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 402 Ramachandran restraints generated. 201 Oldfield, 0 Emsley, 201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 402 Ramachandran restraints generated. 201 Oldfield, 0 Emsley, 201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 17 time to evaluate : 0.129 Fit side-chains revert: symmetry clash REVERT: B 128 LYS cc_start: 0.7844 (mmmt) cc_final: 0.7386 (mmtm) REVERT: B 131 ASN cc_start: 0.8107 (t0) cc_final: 0.7868 (t0) REVERT: C 128 LYS cc_start: 0.7692 (mmmt) cc_final: 0.7331 (tptt) REVERT: C 131 ASN cc_start: 0.8717 (t0) cc_final: 0.8325 (t0) outliers start: 6 outliers final: 5 residues processed: 18 average time/residue: 0.1415 time to fit residues: 2.9967 Evaluate side-chains 23 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 18 time to evaluate : 0.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 112 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 3 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 6 optimal weight: 10.0000 chunk 9 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 chunk 13 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 12 optimal weight: 9.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- 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 = 0.3702 r_free = 0.3702 target = 0.102586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.088947 restraints weight = 2320.832| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 2.71 r_work: 0.3443 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3345 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.2201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 1449 Z= 0.314 Angle : 0.663 5.813 1950 Z= 0.365 Chirality : 0.048 0.119 237 Planarity : 0.002 0.016 261 Dihedral : 4.709 15.511 210 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.41 % Favored : 82.59 % Rotamer: Outliers : 3.21 % Allowed : 19.23 % Favored : 77.56 % 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: -4.92 (0.48), residues: 201 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.75 (0.37), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.002 HIS A 120 ARG 0.001 0.000 ARG B 143 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1030.81 seconds wall clock time: 19 minutes 23.69 seconds (1163.69 seconds total)