Starting phenix.real_space_refine on Wed Mar 5 14:17:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ihv_35460/03_2025/8ihv_35460.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ihv_35460/03_2025/8ihv_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/cci-nas-00/data/ceres_data/8ihv_35460/03_2025/8ihv_35460.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ihv_35460/03_2025/8ihv_35460.map" model { file = "/net/cci-nas-00/data/ceres_data/8ihv_35460/03_2025/8ihv_35460.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ihv_35460/03_2025/8ihv_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-5624/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: 1.14, per 1000 atoms: 0.79 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: 1.27 Conformation dependent library (CDL) restraints added in 239.6 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: 0.16 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: 0.26 Time building geometry restraints manager: 1.33 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' } 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: 2.790 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: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 9.870 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.000 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: 15.450 ------------------------------------------------------------------------------- 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 : 0.169 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: 0.1918 time to fit residues: 7.5926 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 : 0.165 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.103335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.089544 restraints weight = 2315.372| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 2.60 r_work: 0.3463 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3360 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 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 : 0.178 Fit side-chains revert: symmetry clash REVERT: A 112 ILE cc_start: 0.8769 (OUTLIER) cc_final: 0.8121 (mt) REVERT: A 143 ARG cc_start: 0.8726 (ttt180) cc_final: 0.6385 (mtm180) REVERT: B 112 ILE cc_start: 0.8425 (OUTLIER) cc_final: 0.7790 (mt) REVERT: B 128 LYS cc_start: 0.8024 (mmmt) cc_final: 0.7602 (mmtp) REVERT: B 131 ASN cc_start: 0.8381 (t0) cc_final: 0.8147 (t0) REVERT: C 112 ILE cc_start: 0.8294 (OUTLIER) cc_final: 0.7758 (mt) REVERT: C 128 LYS cc_start: 0.7985 (mmmt) cc_final: 0.7619 (tptt) REVERT: C 131 ASN cc_start: 0.8814 (t0) cc_final: 0.8439 (t0) outliers start: 6 outliers final: 2 residues processed: 30 average time/residue: 0.2014 time to fit residues: 6.6726 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 : 0.177 ------------------------------------------------------------------------------- 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 8 optimal weight: 6.9990 chunk 12 optimal weight: 9.9990 chunk 16 optimal weight: 0.0040 chunk 10 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 1 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 5 optimal weight: 0.6980 chunk 17 optimal weight: 3.9990 overall best weight: 1.5396 ------------------------------------------------------------------------------- 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 = 0.3709 r_free = 0.3709 target = 0.102573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.088251 restraints weight = 2289.081| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 2.69 r_work: 0.3437 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3332 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.1652 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= 0.278 Angle : 0.640 6.883 1950 Z= 0.341 Chirality : 0.048 0.123 237 Planarity : 0.002 0.010 261 Dihedral : 4.799 15.913 210 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 19.90 % Favored : 80.10 % Rotamer: Outliers : 6.41 % Allowed : 15.38 % 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: -5.24 (0.47), residues: 201 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.99 (0.36), 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 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 33 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 23 time to evaluate : 0.171 Fit side-chains revert: symmetry clash REVERT: A 143 ARG cc_start: 0.8749 (ttt180) cc_final: 0.6348 (mtm180) REVERT: B 128 LYS cc_start: 0.8109 (mmmt) cc_final: 0.7675 (mmtm) REVERT: B 131 ASN cc_start: 0.8356 (t0) cc_final: 0.8136 (t0) REVERT: B 133 GLU cc_start: 0.8395 (mm-30) cc_final: 0.8178 (mm-30) REVERT: C 128 LYS cc_start: 0.7909 (mmmt) cc_final: 0.7555 (tptt) REVERT: C 131 ASN cc_start: 0.8887 (t0) cc_final: 0.8516 (t0) outliers start: 10 outliers final: 5 residues processed: 28 average time/residue: 0.1865 time to fit residues: 5.8305 Evaluate side-chains 28 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 23 time to evaluate : 0.156 ------------------------------------------------------------------------------- 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 11 optimal weight: 5.9990 chunk 6 optimal weight: 10.0000 chunk 14 optimal weight: 2.9990 chunk 13 optimal weight: 5.9990 chunk 0 optimal weight: 0.7980 chunk 8 optimal weight: 0.9990 chunk 16 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 7 optimal weight: 0.8980 chunk 2 optimal weight: 2.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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 = 0.3714 r_free = 0.3714 target = 0.103011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.088895 restraints weight = 2289.295| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 2.74 r_work: 0.3448 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3346 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.1821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 1449 Z= 0.276 Angle : 0.644 7.693 1950 Z= 0.342 Chirality : 0.048 0.122 237 Planarity : 0.002 0.012 261 Dihedral : 4.757 15.590 210 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.41 % Favored : 82.59 % Rotamer: Outliers : 5.13 % Allowed : 15.38 % 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: -5.16 (0.46), residues: 201 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.93 (0.35), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 110 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 31 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 23 time to evaluate : 0.157 Fit side-chains revert: symmetry clash REVERT: A 143 ARG cc_start: 0.8774 (ttt180) cc_final: 0.6348 (mtm180) REVERT: B 128 LYS cc_start: 0.8133 (mmmt) cc_final: 0.7662 (mmtm) REVERT: B 131 ASN cc_start: 0.8339 (t0) cc_final: 0.8112 (t0) REVERT: B 133 GLU cc_start: 0.8389 (mm-30) cc_final: 0.8139 (mm-30) REVERT: C 128 LYS cc_start: 0.8016 (mmmt) cc_final: 0.7630 (tptt) REVERT: C 131 ASN cc_start: 0.8882 (t0) cc_final: 0.8491 (t0) outliers start: 8 outliers final: 5 residues processed: 25 average time/residue: 0.1902 time to fit residues: 5.2924 Evaluate side-chains 28 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 23 time to evaluate : 0.155 ------------------------------------------------------------------------------- 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 13 optimal weight: 4.9990 chunk 16 optimal weight: 5.9990 chunk 15 optimal weight: 0.9990 chunk 3 optimal weight: 2.9990 chunk 10 optimal weight: 5.9990 chunk 9 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 4 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 17 optimal weight: 0.0370 overall best weight: 1.8066 ------------------------------------------------------------------------------- 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 = 0.3685 r_free = 0.3685 target = 0.101677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.087564 restraints weight = 2304.459| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 2.69 r_work: 0.3421 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3320 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.1946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 1449 Z= 0.320 Angle : 0.670 7.858 1950 Z= 0.357 Chirality : 0.049 0.124 237 Planarity : 0.002 0.011 261 Dihedral : 4.961 15.557 210 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 19.90 % Favored : 80.10 % Rotamer: Outliers : 4.49 % Allowed : 17.95 % 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: -5.16 (0.46), residues: 201 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.92 (0.35), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.002 HIS A 120 ARG 0.001 0.000 ARG A 143 *********************** 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 30 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 23 time to evaluate : 0.158 Fit side-chains revert: symmetry clash REVERT: A 143 ARG cc_start: 0.8781 (ttt180) cc_final: 0.6347 (mtm180) REVERT: B 128 LYS cc_start: 0.8061 (mmmt) cc_final: 0.7610 (mmtm) REVERT: B 131 ASN cc_start: 0.8347 (t0) cc_final: 0.8136 (t0) REVERT: B 133 GLU cc_start: 0.8403 (mm-30) cc_final: 0.8185 (mm-30) REVERT: C 128 LYS cc_start: 0.7957 (mmmt) cc_final: 0.7583 (tptt) REVERT: C 131 ASN cc_start: 0.8899 (t0) cc_final: 0.8513 (t0) outliers start: 7 outliers final: 5 residues processed: 24 average time/residue: 0.2224 time to fit residues: 5.8635 Evaluate side-chains 28 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 23 time to evaluate : 0.139 ------------------------------------------------------------------------------- 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 3 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 10 optimal weight: 6.9990 chunk 15 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 12 optimal weight: 5.9990 chunk 7 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 4 optimal weight: 0.8980 overall best weight: 1.9786 ------------------------------------------------------------------------------- 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 = 0.3670 r_free = 0.3670 target = 0.101099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.086970 restraints weight = 2321.975| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 2.73 r_work: 0.3409 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3306 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.1993 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= 0.349 Angle : 0.691 8.194 1950 Z= 0.371 Chirality : 0.049 0.123 237 Planarity : 0.003 0.018 261 Dihedral : 5.085 16.298 210 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 19.40 % Favored : 80.60 % Rotamer: Outliers : 5.13 % Allowed : 19.23 % Favored : 75.64 % 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: -5.18 (0.46), residues: 201 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.94 (0.35), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.002 HIS A 120 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 30 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 22 time to evaluate : 0.166 Fit side-chains revert: symmetry clash REVERT: A 143 ARG cc_start: 0.8789 (ttt180) cc_final: 0.6326 (mtm180) REVERT: B 128 LYS cc_start: 0.8096 (mmmt) cc_final: 0.7631 (mmtm) REVERT: B 131 ASN cc_start: 0.8399 (t0) cc_final: 0.8191 (t0) REVERT: B 133 GLU cc_start: 0.8406 (mm-30) cc_final: 0.8174 (mm-30) REVERT: C 128 LYS cc_start: 0.7968 (mmmt) cc_final: 0.7606 (tptt) REVERT: C 131 ASN cc_start: 0.8903 (t0) cc_final: 0.8513 (t0) outliers start: 8 outliers final: 5 residues processed: 24 average time/residue: 0.2017 time to fit residues: 5.4057 Evaluate side-chains 26 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 21 time to evaluate : 0.171 ------------------------------------------------------------------------------- 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 13 optimal weight: 0.0870 chunk 0 optimal weight: 10.0000 chunk 7 optimal weight: 5.9990 chunk 11 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 overall best weight: 1.8166 ------------------------------------------------------------------------------- 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 = 0.3683 r_free = 0.3683 target = 0.101680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.087627 restraints weight = 2369.325| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 2.74 r_work: 0.3423 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3321 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.2071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 1449 Z= 0.321 Angle : 0.730 10.971 1950 Z= 0.374 Chirality : 0.049 0.144 237 Planarity : 0.003 0.015 261 Dihedral : 4.959 16.049 210 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 20.90 % Favored : 79.10 % Rotamer: Outliers : 3.85 % Allowed : 21.15 % Favored : 75.00 % 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: -5.14 (0.46), residues: 201 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.91 (0.35), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.002 HIS A 120 ARG 0.003 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 28 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 22 time to evaluate : 0.162 Fit side-chains revert: symmetry clash REVERT: A 143 ARG cc_start: 0.8808 (ttt180) cc_final: 0.6395 (mtm180) REVERT: B 128 LYS cc_start: 0.8084 (mmmt) cc_final: 0.7641 (mmtm) REVERT: B 133 GLU cc_start: 0.8374 (mm-30) cc_final: 0.8164 (mm-30) REVERT: C 128 LYS cc_start: 0.7942 (mmmt) cc_final: 0.7590 (tptt) REVERT: C 131 ASN cc_start: 0.8880 (t0) cc_final: 0.8498 (t0) outliers start: 6 outliers final: 5 residues processed: 23 average time/residue: 0.2239 time to fit residues: 5.7530 Evaluate side-chains 26 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 21 time to evaluate : 0.162 ------------------------------------------------------------------------------- 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 14 optimal weight: 3.9990 chunk 10 optimal weight: 8.9990 chunk 1 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 6 optimal weight: 10.0000 chunk 7 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- 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 = 0.3648 r_free = 0.3648 target = 0.099731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.085888 restraints weight = 2356.406| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 2.65 r_work: 0.3389 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3288 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.2087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.034 1449 Z= 0.415 Angle : 0.794 9.845 1950 Z= 0.418 Chirality : 0.051 0.134 237 Planarity : 0.003 0.009 261 Dihedral : 5.354 17.952 210 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 20.90 % Favored : 79.10 % Rotamer: Outliers : 3.85 % Allowed : 21.15 % Favored : 75.00 % 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: -5.22 (0.46), residues: 201 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.97 (0.35), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS A 120 ARG 0.002 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 27 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 21 time to evaluate : 0.164 Fit side-chains revert: symmetry clash REVERT: A 143 ARG cc_start: 0.8807 (ttt180) cc_final: 0.6448 (mtm180) REVERT: B 128 LYS cc_start: 0.8138 (mmmt) cc_final: 0.7679 (mmtm) REVERT: B 133 GLU cc_start: 0.8453 (mm-30) cc_final: 0.8226 (mm-30) REVERT: C 128 LYS cc_start: 0.7972 (mmmt) cc_final: 0.7620 (tptt) REVERT: C 131 ASN cc_start: 0.8896 (t0) cc_final: 0.8508 (t0) outliers start: 6 outliers final: 6 residues processed: 22 average time/residue: 0.1698 time to fit residues: 4.2685 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 : 0.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 144 LEU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 13 optimal weight: 4.9990 chunk 1 optimal weight: 4.9990 chunk 15 optimal weight: 0.6980 chunk 4 optimal weight: 5.9990 chunk 14 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 chunk 16 optimal weight: 5.9990 chunk 6 optimal weight: 6.9990 chunk 0 optimal weight: 0.9980 chunk 7 optimal weight: 0.8980 chunk 8 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 = 0.3748 r_free = 0.3748 target = 0.104729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.090900 restraints weight = 2346.935| |-----------------------------------------------------------------------------| r_work (start): 0.3583 rms_B_bonded: 2.80 r_work: 0.3490 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3389 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.2254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 1449 Z= 0.190 Angle : 0.668 9.049 1950 Z= 0.346 Chirality : 0.048 0.117 237 Planarity : 0.002 0.011 261 Dihedral : 4.297 16.099 210 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 2.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.42 % Favored : 84.58 % Rotamer: Outliers : 3.21 % Allowed : 21.79 % Favored : 75.00 % 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: -4.89 (0.49), residues: 201 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.72 (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 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 25 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 20 time to evaluate : 0.157 Fit side-chains revert: symmetry clash REVERT: A 143 ARG cc_start: 0.8736 (ttt180) cc_final: 0.6323 (mtm180) REVERT: B 128 LYS cc_start: 0.8136 (mmmt) cc_final: 0.7658 (mmtm) REVERT: B 133 GLU cc_start: 0.8346 (mm-30) cc_final: 0.8093 (mm-30) REVERT: C 128 LYS cc_start: 0.8021 (mmmt) cc_final: 0.7642 (tptt) outliers start: 5 outliers final: 4 residues processed: 20 average time/residue: 0.2850 time to fit residues: 6.2665 Evaluate side-chains 23 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 19 time to evaluate : 0.139 ------------------------------------------------------------------------------- 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 1 optimal weight: 3.9990 chunk 4 optimal weight: 5.9990 chunk 12 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 11 optimal weight: 5.9990 chunk 3 optimal weight: 5.9990 chunk 13 optimal weight: 0.9990 chunk 14 optimal weight: 6.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- 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 = 0.3706 r_free = 0.3706 target = 0.102853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.088978 restraints weight = 2360.399| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 2.75 r_work: 0.3446 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3346 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.2143 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= 0.284 Angle : 0.706 9.659 1950 Z= 0.366 Chirality : 0.049 0.137 237 Planarity : 0.002 0.009 261 Dihedral : 4.661 16.261 210 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 1.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 20.40 % Favored : 79.60 % Rotamer: Outliers : 3.21 % Allowed : 20.51 % Favored : 76.28 % 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: -4.94 (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 0.002 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 25 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 20 time to evaluate : 0.163 Fit side-chains revert: symmetry clash REVERT: A 143 ARG cc_start: 0.8771 (ttt180) cc_final: 0.6387 (mtm180) REVERT: B 128 LYS cc_start: 0.8078 (mmmt) cc_final: 0.7646 (mmtm) REVERT: B 133 GLU cc_start: 0.8394 (mm-30) cc_final: 0.8180 (mm-30) REVERT: C 128 LYS cc_start: 0.7949 (mmmt) cc_final: 0.7592 (tptt) REVERT: C 131 ASN cc_start: 0.8861 (t0) cc_final: 0.8475 (t0) outliers start: 5 outliers final: 5 residues processed: 21 average time/residue: 0.2269 time to fit residues: 5.2953 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 : 0.164 ------------------------------------------------------------------------------- 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 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 14 optimal weight: 5.9990 chunk 10 optimal weight: 7.9990 chunk 6 optimal weight: 7.9990 chunk 3 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 8 optimal weight: 0.8980 chunk 11 optimal weight: 0.6980 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 = 0.3744 r_free = 0.3744 target = 0.104751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.090939 restraints weight = 2378.842| |-----------------------------------------------------------------------------| r_work (start): 0.3580 rms_B_bonded: 2.75 r_work: 0.3485 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3385 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.2310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 1449 Z= 0.215 Angle : 0.660 9.284 1950 Z= 0.341 Chirality : 0.048 0.119 237 Planarity : 0.002 0.014 261 Dihedral : 4.327 15.858 210 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 1.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.92 % Favored : 84.08 % Rotamer: Outliers : 3.21 % Allowed : 20.51 % Favored : 76.28 % 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: -4.86 (0.49), residues: 201 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.70 (0.38), 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 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1341.06 seconds wall clock time: 23 minutes 48.84 seconds (1428.84 seconds total)