Starting phenix.real_space_refine on Wed Mar 5 22:30:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6zrq_11382/03_2025/6zrq_11382.cif Found real_map, /net/cci-nas-00/data/ceres_data/6zrq_11382/03_2025/6zrq_11382.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6zrq_11382/03_2025/6zrq_11382.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6zrq_11382/03_2025/6zrq_11382.map" model { file = "/net/cci-nas-00/data/ceres_data/6zrq_11382/03_2025/6zrq_11382.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6zrq_11382/03_2025/6zrq_11382.cif" } resolution = 3.9 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 C 1272 2.51 5 N 360 2.21 5 O 408 1.98 5 H 1908 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 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: 3948 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 329 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 329 Classifications: {'peptide': 23} Link IDs: {'TRANS': 22} Restraints were copied for chains: C, B, E, D, G, F, I, H, K, J, L Time building chain proxies: 1.79, per 1000 atoms: 0.45 Number of scatterers: 3948 At special positions: 0 Unit cell: (50.055, 79.875, 44.73, 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) O 408 8.00 N 360 7.00 C 1272 6.00 H 1908 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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: 1.08 Conformation dependent library (CDL) restraints added in 253.1 milliseconds 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 480 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 0 helices and 0 sheets defined 0.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.64 Creating SS restraints... No hydrogen bonds defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.00 Time building geometry restraints manager: 1.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 0.97: 1753 0.97 - 1.12: 155 1.12 - 1.26: 324 1.26 - 1.40: 612 1.40 - 1.54: 1140 Bond restraints: 3984 Sorted by residual: bond pdb=" N TYC H 37 " pdb=" H TYC H 37 " ideal model delta sigma weight residual 0.860 1.030 -0.170 2.00e-02 2.50e+03 7.25e+01 bond pdb=" N TYC L 37 " pdb=" H TYC L 37 " ideal model delta sigma weight residual 0.860 1.030 -0.170 2.00e-02 2.50e+03 7.23e+01 bond pdb=" N TYC A 37 " pdb=" H TYC A 37 " ideal model delta sigma weight residual 0.860 1.030 -0.170 2.00e-02 2.50e+03 7.23e+01 bond pdb=" N TYC K 37 " pdb=" H TYC K 37 " ideal model delta sigma weight residual 0.860 1.030 -0.170 2.00e-02 2.50e+03 7.22e+01 bond pdb=" N TYC C 37 " pdb=" H TYC C 37 " ideal model delta sigma weight residual 0.860 1.030 -0.170 2.00e-02 2.50e+03 7.21e+01 ... (remaining 3979 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.35: 6815 2.35 - 4.71: 187 4.71 - 7.06: 6 7.06 - 9.42: 0 9.42 - 11.77: 12 Bond angle restraints: 7020 Sorted by residual: angle pdb=" CA LEU I 16 " pdb=" CB LEU I 16 " pdb=" CG LEU I 16 " ideal model delta sigma weight residual 116.30 128.07 -11.77 3.50e+00 8.16e-02 1.13e+01 angle pdb=" CA LEU K 16 " pdb=" CB LEU K 16 " pdb=" CG LEU K 16 " ideal model delta sigma weight residual 116.30 128.05 -11.75 3.50e+00 8.16e-02 1.13e+01 angle pdb=" CA LEU C 16 " pdb=" CB LEU C 16 " pdb=" CG LEU C 16 " ideal model delta sigma weight residual 116.30 128.04 -11.74 3.50e+00 8.16e-02 1.13e+01 angle pdb=" CA LEU D 16 " pdb=" CB LEU D 16 " pdb=" CG LEU D 16 " ideal model delta sigma weight residual 116.30 128.03 -11.73 3.50e+00 8.16e-02 1.12e+01 angle pdb=" CA LEU F 16 " pdb=" CB LEU F 16 " pdb=" CG LEU F 16 " ideal model delta sigma weight residual 116.30 128.03 -11.73 3.50e+00 8.16e-02 1.12e+01 ... (remaining 7015 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.47: 1500 12.47 - 24.93: 312 24.93 - 37.40: 36 37.40 - 49.86: 36 49.86 - 62.33: 48 Dihedral angle restraints: 1932 sinusoidal: 1032 harmonic: 900 Sorted by residual: dihedral pdb=" CA SER D 19 " pdb=" C SER D 19 " pdb=" N GLY D 20 " pdb=" CA GLY D 20 " ideal model delta harmonic sigma weight residual 180.00 153.81 26.19 0 5.00e+00 4.00e-02 2.74e+01 dihedral pdb=" CA SER H 19 " pdb=" C SER H 19 " pdb=" N GLY H 20 " pdb=" CA GLY H 20 " ideal model delta harmonic sigma weight residual 180.00 153.82 26.18 0 5.00e+00 4.00e-02 2.74e+01 dihedral pdb=" CA SER B 19 " pdb=" C SER B 19 " pdb=" N GLY B 20 " pdb=" CA GLY B 20 " ideal model delta harmonic sigma weight residual 180.00 153.83 26.17 0 5.00e+00 4.00e-02 2.74e+01 ... (remaining 1929 not shown) Histogram of chiral volume deviations from ideal: 0.004 - 0.022: 112 0.022 - 0.041: 92 0.041 - 0.059: 27 0.059 - 0.078: 81 0.078 - 0.096: 12 Chirality restraints: 324 Sorted by residual: chirality pdb=" CA PHE D 23 " pdb=" N PHE D 23 " pdb=" C PHE D 23 " pdb=" CB PHE D 23 " both_signs ideal model delta sigma weight residual False 2.51 2.61 -0.10 2.00e-01 2.50e+01 2.30e-01 chirality pdb=" CA PHE H 23 " pdb=" N PHE H 23 " pdb=" C PHE H 23 " pdb=" CB PHE H 23 " both_signs ideal model delta sigma weight residual False 2.51 2.61 -0.10 2.00e-01 2.50e+01 2.29e-01 chirality pdb=" CA PHE I 23 " pdb=" N PHE I 23 " pdb=" C PHE I 23 " pdb=" CB PHE I 23 " both_signs ideal model delta sigma weight residual False 2.51 2.61 -0.10 2.00e-01 2.50e+01 2.28e-01 ... (remaining 321 not shown) Planarity restraints: 636 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS K 18 " -0.001 2.00e-02 2.50e+03 6.31e-03 8.96e-01 pdb=" CG HIS K 18 " -0.010 2.00e-02 2.50e+03 pdb=" ND1 HIS K 18 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 HIS K 18 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 HIS K 18 " -0.007 2.00e-02 2.50e+03 pdb=" NE2 HIS K 18 " 0.000 2.00e-02 2.50e+03 pdb=" HD1 HIS K 18 " -0.001 2.00e-02 2.50e+03 pdb=" HD2 HIS K 18 " 0.001 2.00e-02 2.50e+03 pdb=" HE1 HIS K 18 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS L 18 " 0.001 2.00e-02 2.50e+03 6.28e-03 8.88e-01 pdb=" CG HIS L 18 " 0.010 2.00e-02 2.50e+03 pdb=" ND1 HIS L 18 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 HIS L 18 " -0.006 2.00e-02 2.50e+03 pdb=" CE1 HIS L 18 " 0.006 2.00e-02 2.50e+03 pdb=" NE2 HIS L 18 " 0.001 2.00e-02 2.50e+03 pdb=" HD1 HIS L 18 " 0.001 2.00e-02 2.50e+03 pdb=" HD2 HIS L 18 " -0.001 2.00e-02 2.50e+03 pdb=" HE1 HIS L 18 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS E 18 " -0.001 2.00e-02 2.50e+03 6.22e-03 8.70e-01 pdb=" CG HIS E 18 " -0.010 2.00e-02 2.50e+03 pdb=" ND1 HIS E 18 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 HIS E 18 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 HIS E 18 " -0.007 2.00e-02 2.50e+03 pdb=" NE2 HIS E 18 " 0.000 2.00e-02 2.50e+03 pdb=" HD1 HIS E 18 " -0.001 2.00e-02 2.50e+03 pdb=" HD2 HIS E 18 " 0.001 2.00e-02 2.50e+03 pdb=" HE1 HIS E 18 " -0.001 2.00e-02 2.50e+03 ... (remaining 633 not shown) Histogram of nonbonded interaction distances: 1.73 - 2.28: 813 2.28 - 2.84: 8947 2.84 - 3.39: 9216 3.39 - 3.95: 13796 3.95 - 4.50: 18435 Nonbonded interactions: 51207 Sorted by model distance: nonbonded pdb=" HA TYC J 37 " pdb="HT21 TYC L 37 " model vdw 1.731 2.270 nonbonded pdb=" HA TYC B 37 " pdb="HT21 TYC D 37 " model vdw 1.765 2.270 nonbonded pdb=" HA TYC I 37 " pdb="HT21 TYC K 37 " model vdw 1.789 2.270 nonbonded pdb=" HA TYC F 37 " pdb="HT21 TYC H 37 " model vdw 1.810 2.270 nonbonded pdb=" HA TYC C 37 " pdb="HT21 TYC E 37 " model vdw 1.812 2.270 ... (remaining 51202 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' selection = chain 'I' selection = chain 'H' selection = chain 'K' selection = chain 'J' selection = chain 'L' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.550 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: 0.080 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 11.880 Find NCS groups from input model: 0.070 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6279 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.035 2076 Z= 0.401 Angle : 1.220 11.770 2820 Z= 0.531 Chirality : 0.045 0.096 324 Planarity : 0.004 0.008 372 Dihedral : 11.935 26.190 684 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 20.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.20 (0.39), residues: 240 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.19 (0.30), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.012 0.007 HIS K 18 PHE 0.008 0.004 PHE A 15 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 0.328 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 15 PHE cc_start: 0.4850 (t80) cc_final: 0.4619 (m-80) REVERT: I 16 LEU cc_start: 0.6021 (pt) cc_final: 0.5482 (pt) REVERT: K 29 SER cc_start: 0.7769 (t) cc_final: 0.7472 (p) REVERT: K 36 THR cc_start: 0.7643 (t) cc_final: 0.7437 (t) REVERT: L 36 THR cc_start: 0.7117 (t) cc_final: 0.6912 (t) outliers start: 0 outliers final: 0 residues processed: 59 average time/residue: 0.1294 time to fit residues: 10.1626 Evaluate side-chains 20 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 20 optimal weight: 0.9980 chunk 18 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 chunk 6 optimal weight: 0.9990 chunk 12 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 7 optimal weight: 0.5980 chunk 11 optimal weight: 0.5980 chunk 14 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4624 r_free = 0.4624 target = 0.112453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4465 r_free = 0.4465 target = 0.104579 restraints weight = 18817.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4513 r_free = 0.4513 target = 0.107176 restraints weight = 6436.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4545 r_free = 0.4545 target = 0.108723 restraints weight = 3108.059| |-----------------------------------------------------------------------------| r_work (final): 0.4548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7416 moved from start: 0.3255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.016 2076 Z= 0.135 Angle : 0.584 3.702 2820 Z= 0.312 Chirality : 0.045 0.119 324 Planarity : 0.002 0.007 372 Dihedral : 8.100 19.269 348 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 1.85 % Allowed : 19.44 % Favored : 78.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.26 (0.40), residues: 240 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.24 (0.31), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS K 18 PHE 0.014 0.002 PHE D 15 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 33 time to evaluate : 0.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 4 residues processed: 37 average time/residue: 0.1296 time to fit residues: 6.6224 Evaluate side-chains 20 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 16 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 21 ASN Chi-restraints excluded: chain I residue 21 ASN Chi-restraints excluded: chain J residue 15 PHE Chi-restraints excluded: chain K residue 21 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 5 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 20 optimal weight: 0.0170 chunk 6 optimal weight: 0.2980 chunk 16 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 chunk 9 optimal weight: 0.5980 overall best weight: 0.5820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4715 r_free = 0.4715 target = 0.146134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4844 r_free = 0.4844 target = 0.124172 restraints weight = 17160.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4901 r_free = 0.4901 target = 0.126863 restraints weight = 7062.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4933 r_free = 0.4933 target = 0.128370 restraints weight = 3799.316| |-----------------------------------------------------------------------------| r_work (final): 0.4485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.4490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 2076 Z= 0.103 Angle : 0.522 3.388 2820 Z= 0.280 Chirality : 0.042 0.119 324 Planarity : 0.002 0.005 372 Dihedral : 6.658 26.231 348 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 0.93 % Allowed : 23.61 % Favored : 75.46 % 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: -4.63 (0.34), residues: 240 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.52 (0.26), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS H 18 PHE 0.011 0.001 PHE H 15 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 23 time to evaluate : 0.270 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 25 average time/residue: 0.1298 time to fit residues: 4.6000 Evaluate side-chains 15 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 13 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 29 SER Chi-restraints excluded: chain J residue 15 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 14 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 2 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 0 optimal weight: 0.5980 chunk 12 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 22 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4368 r_free = 0.4368 target = 0.099145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.091475 restraints weight = 21296.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.093880 restraints weight = 7949.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.095304 restraints weight = 3900.739| |-----------------------------------------------------------------------------| r_work (final): 0.4280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.5244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.020 2076 Z= 0.160 Angle : 0.569 4.366 2820 Z= 0.312 Chirality : 0.043 0.115 324 Planarity : 0.002 0.006 372 Dihedral : 7.015 26.134 348 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 14.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 4.17 % Allowed : 26.85 % Favored : 68.98 % 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: -5.05 (0.31), residues: 240 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.85 (0.24), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS K 18 PHE 0.012 0.002 PHE J 23 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 13 time to evaluate : 0.333 Fit side-chains outliers start: 9 outliers final: 6 residues processed: 22 average time/residue: 0.1059 time to fit residues: 3.5713 Evaluate side-chains 19 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 13 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 23 PHE Chi-restraints excluded: chain E residue 29 SER Chi-restraints excluded: chain H residue 29 SER Chi-restraints excluded: chain I residue 29 SER Chi-restraints excluded: chain J residue 15 PHE Chi-restraints excluded: chain K residue 21 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 0 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 23 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 7 optimal weight: 0.3980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.094150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.087041 restraints weight = 22469.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.089278 restraints weight = 8313.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.090621 restraints weight = 4059.838| |-----------------------------------------------------------------------------| r_work (final): 0.4196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.5867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.020 2076 Z= 0.184 Angle : 0.587 3.964 2820 Z= 0.326 Chirality : 0.044 0.124 324 Planarity : 0.003 0.008 372 Dihedral : 7.322 26.378 348 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 19.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.08 % Favored : 87.92 % Rotamer: Outliers : 3.70 % Allowed : 28.24 % Favored : 68.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.23 (0.33), residues: 240 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.98 (0.25), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS J 18 PHE 0.009 0.002 PHE C 23 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 19 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 11 time to evaluate : 0.297 Fit side-chains outliers start: 8 outliers final: 5 residues processed: 18 average time/residue: 0.1064 time to fit residues: 3.0267 Evaluate side-chains 15 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 10 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 23 PHE Chi-restraints excluded: chain I residue 21 ASN Chi-restraints excluded: chain J residue 15 PHE Chi-restraints excluded: chain J residue 36 THR Chi-restraints excluded: chain K residue 36 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 12 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 6 optimal weight: 2.9990 chunk 5 optimal weight: 0.6980 chunk 17 optimal weight: 0.8980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.096064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.088964 restraints weight = 21809.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.091252 restraints weight = 7888.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.092650 restraints weight = 3814.568| |-----------------------------------------------------------------------------| r_work (final): 0.4221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.6088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.015 2076 Z= 0.130 Angle : 0.519 4.121 2820 Z= 0.289 Chirality : 0.043 0.125 324 Planarity : 0.002 0.005 372 Dihedral : 6.783 25.456 348 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 18.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.83 % Favored : 89.17 % Rotamer: Outliers : 4.17 % Allowed : 25.93 % Favored : 69.91 % 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: -5.23 (0.33), residues: 240 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.98 (0.25), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS J 18 PHE 0.009 0.001 PHE C 23 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 21 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 12 time to evaluate : 0.295 Fit side-chains REVERT: I 15 PHE cc_start: 0.5610 (OUTLIER) cc_final: 0.3929 (m-80) outliers start: 9 outliers final: 6 residues processed: 21 average time/residue: 0.1044 time to fit residues: 3.3689 Evaluate side-chains 18 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 11 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 23 PHE Chi-restraints excluded: chain E residue 29 SER Chi-restraints excluded: chain I residue 15 PHE Chi-restraints excluded: chain I residue 16 LEU Chi-restraints excluded: chain I residue 29 SER Chi-restraints excluded: chain J residue 15 PHE Chi-restraints excluded: chain J residue 36 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 7 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 19 optimal weight: 0.5980 chunk 22 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 overall best weight: 1.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.093830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.086952 restraints weight = 22086.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.089179 restraints weight = 8094.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.090550 restraints weight = 3929.199| |-----------------------------------------------------------------------------| r_work (final): 0.4195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.6411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.017 2076 Z= 0.166 Angle : 0.555 3.874 2820 Z= 0.310 Chirality : 0.043 0.126 324 Planarity : 0.002 0.006 372 Dihedral : 6.963 24.827 348 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 21.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.08 % Favored : 82.92 % Rotamer: Outliers : 4.17 % Allowed : 26.85 % Favored : 68.98 % 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: -5.39 (0.33), residues: 240 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.11 (0.25), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS H 18 PHE 0.009 0.001 PHE C 23 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 21 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 12 time to evaluate : 0.254 Fit side-chains REVERT: I 15 PHE cc_start: 0.5622 (OUTLIER) cc_final: 0.3729 (m-80) outliers start: 9 outliers final: 8 residues processed: 19 average time/residue: 0.1042 time to fit residues: 3.0296 Evaluate side-chains 21 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 12 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 23 PHE Chi-restraints excluded: chain E residue 29 SER Chi-restraints excluded: chain H residue 29 SER Chi-restraints excluded: chain I residue 15 PHE Chi-restraints excluded: chain I residue 16 LEU Chi-restraints excluded: chain I residue 21 ASN Chi-restraints excluded: chain J residue 15 PHE Chi-restraints excluded: chain J residue 36 THR Chi-restraints excluded: chain K residue 36 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 5 optimal weight: 0.7980 chunk 23 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.094923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.088204 restraints weight = 21955.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.090408 restraints weight = 7948.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.091761 restraints weight = 3878.560| |-----------------------------------------------------------------------------| r_work (final): 0.4208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.6589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.015 2076 Z= 0.137 Angle : 0.522 3.915 2820 Z= 0.293 Chirality : 0.043 0.126 324 Planarity : 0.002 0.005 372 Dihedral : 6.682 24.574 348 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 21.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.67 % Favored : 88.33 % Rotamer: Outliers : 4.17 % Allowed : 26.39 % Favored : 69.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.43 (0.32), residues: 240 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.14 (0.24), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS K 18 PHE 0.007 0.001 PHE C 23 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 13 time to evaluate : 0.334 Fit side-chains outliers start: 9 outliers final: 9 residues processed: 19 average time/residue: 0.1133 time to fit residues: 3.3328 Evaluate side-chains 21 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 12 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 23 PHE Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain E residue 29 SER Chi-restraints excluded: chain I residue 15 PHE Chi-restraints excluded: chain I residue 16 LEU Chi-restraints excluded: chain I residue 29 SER Chi-restraints excluded: chain J residue 15 PHE Chi-restraints excluded: chain J residue 36 THR Chi-restraints excluded: chain K residue 36 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 10 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 13 optimal weight: 0.0980 chunk 7 optimal weight: 0.8980 chunk 12 optimal weight: 0.9980 chunk 8 optimal weight: 0.5980 chunk 19 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 23 optimal weight: 0.6980 chunk 16 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.097181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.090283 restraints weight = 21591.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.092506 restraints weight = 8000.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.093878 restraints weight = 3801.819| |-----------------------------------------------------------------------------| r_work (final): 0.4247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.6723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.011 2076 Z= 0.098 Angle : 0.477 3.604 2820 Z= 0.268 Chirality : 0.042 0.124 324 Planarity : 0.002 0.005 372 Dihedral : 6.267 24.473 348 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 20.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.83 % Favored : 89.17 % Rotamer: Outliers : 1.85 % Allowed : 28.24 % Favored : 69.91 % 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: -5.36 (0.33), residues: 240 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.08 (0.25), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS H 18 PHE 0.009 0.001 PHE C 23 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 12 time to evaluate : 0.315 Fit side-chains outliers start: 4 outliers final: 4 residues processed: 16 average time/residue: 0.1116 time to fit residues: 2.8286 Evaluate side-chains 16 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 12 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 23 PHE Chi-restraints excluded: chain I residue 15 PHE Chi-restraints excluded: chain I residue 16 LEU Chi-restraints excluded: chain J residue 15 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 23 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 19 optimal weight: 0.5980 chunk 8 optimal weight: 0.8980 chunk 4 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.096456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.089575 restraints weight = 21593.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.091835 restraints weight = 7807.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.093172 restraints weight = 3772.334| |-----------------------------------------------------------------------------| r_work (final): 0.4234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.6834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.012 2076 Z= 0.114 Angle : 0.484 3.541 2820 Z= 0.272 Chirality : 0.042 0.123 324 Planarity : 0.002 0.005 372 Dihedral : 6.246 23.880 348 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 21.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.83 % Favored : 89.17 % Rotamer: Outliers : 1.85 % Allowed : 28.24 % Favored : 69.91 % 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: -5.40 (0.32), residues: 240 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.11 (0.24), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS H 18 PHE 0.007 0.001 PHE C 23 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 12 time to evaluate : 0.309 Fit side-chains outliers start: 4 outliers final: 4 residues processed: 16 average time/residue: 0.1091 time to fit residues: 2.7583 Evaluate side-chains 16 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 12 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 23 PHE Chi-restraints excluded: chain I residue 15 PHE Chi-restraints excluded: chain I residue 16 LEU Chi-restraints excluded: chain J residue 15 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 9 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 2 optimal weight: 2.9990 chunk 6 optimal weight: 0.6980 chunk 10 optimal weight: 0.9980 chunk 22 optimal weight: 0.9980 chunk 5 optimal weight: 0.2980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.096290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.089379 restraints weight = 21501.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.091646 restraints weight = 7749.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.093067 restraints weight = 3772.074| |-----------------------------------------------------------------------------| r_work (final): 0.4237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.6926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.012 2076 Z= 0.113 Angle : 0.479 3.520 2820 Z= 0.270 Chirality : 0.042 0.124 324 Planarity : 0.002 0.005 372 Dihedral : 6.176 23.797 348 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 21.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.25 % Favored : 88.75 % Rotamer: Outliers : 2.31 % Allowed : 27.31 % Favored : 70.37 % 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: -5.44 (0.32), residues: 240 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.14 (0.24), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS H 18 PHE 0.008 0.001 PHE C 23 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2377.47 seconds wall clock time: 41 minutes 8.84 seconds (2468.84 seconds total)