Starting phenix.real_space_refine on Tue Feb 11 03:19:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6zrq_11382/02_2025/6zrq_11382.cif Found real_map, /net/cci-nas-00/data/ceres_data/6zrq_11382/02_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_11382/02_2025/6zrq_11382.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6zrq_11382/02_2025/6zrq_11382.map" model { file = "/net/cci-nas-00/data/ceres_data/6zrq_11382/02_2025/6zrq_11382.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6zrq_11382/02_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-5592/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: 1.74, per 1000 atoms: 0.44 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: 1.01 Conformation dependent library (CDL) restraints added in 247.7 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: 0.78 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: 1.21 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.840 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: 0.020 Set scattering table: 0.050 Process input model: 11.650 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: 16.770 ------------------------------------------------------------------------------- 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 : 0.248 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: 0.1245 time to fit residues: 9.8166 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 : 0.290 ------------------------------------------------------------------------------- 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 = 0.104578 restraints weight = 18817.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4513 r_free = 0.4513 target = 0.107181 restraints weight = 6436.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4541 r_free = 0.4541 target = 0.108665 restraints weight = 3107.843| |-----------------------------------------------------------------------------| r_work (final): 0.4545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7417 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 : 0.317 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: 0.1260 time to fit residues: 6.4212 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 : 0.324 ------------------------------------------------------------------------------- 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: 0.9980 chunk 23 optimal weight: 0.6980 chunk 13 optimal weight: 2.9990 chunk 20 optimal weight: 0.0570 chunk 6 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 chunk 14 optimal weight: 0.9980 chunk 9 optimal weight: 0.5980 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 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 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 = 0.4698 r_free = 0.4698 target = 0.144272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4818 r_free = 0.4818 target = 0.122349 restraints weight = 17297.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4874 r_free = 0.4874 target = 0.124978 restraints weight = 7132.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4915 r_free = 0.4915 target = 0.126603 restraints weight = 3849.876| |-----------------------------------------------------------------------------| r_work (final): 0.4470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.4558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 2076 Z= 0.115 Angle : 0.539 3.576 2820 Z= 0.290 Chirality : 0.043 0.119 324 Planarity : 0.002 0.006 372 Dihedral : 6.772 26.747 348 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 1.39 % Allowed : 23.15 % 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: -4.72 (0.33), residues: 240 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.59 (0.25), 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 23 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 20 time to evaluate : 0.306 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 23 average time/residue: 0.1444 time to fit residues: 4.5851 Evaluate side-chains 15 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 12 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 29 SER 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: 0.6980 chunk 2 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 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: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4426 r_free = 0.4426 target = 0.102536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.094669 restraints weight = 20672.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.097161 restraints weight = 7655.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.098654 restraints weight = 3763.533| |-----------------------------------------------------------------------------| r_work (final): 0.4338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.5099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2076 Z= 0.125 Angle : 0.505 4.356 2820 Z= 0.278 Chirality : 0.042 0.117 324 Planarity : 0.002 0.005 372 Dihedral : 6.596 25.824 348 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 1.85 % Allowed : 26.85 % Favored : 71.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.99 (0.32), residues: 240 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.80 (0.24), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS K 18 PHE 0.013 0.001 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 17 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 13 time to evaluate : 0.287 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 17 average time/residue: 0.0988 time to fit residues: 2.6749 Evaluate side-chains 15 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 12 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E 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: 2.9990 chunk 12 optimal weight: 2.9990 chunk 22 optimal weight: 0.0970 chunk 23 optimal weight: 0.2980 chunk 17 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 7 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4357 r_free = 0.4357 target = 0.098569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.091072 restraints weight = 21922.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.093433 restraints weight = 7940.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.094812 restraints weight = 3880.513| |-----------------------------------------------------------------------------| r_work (final): 0.4270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.5607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 2076 Z= 0.138 Angle : 0.521 4.564 2820 Z= 0.287 Chirality : 0.042 0.116 324 Planarity : 0.002 0.005 372 Dihedral : 6.755 26.370 348 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 13.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.50 % Favored : 92.50 % Rotamer: Outliers : 3.24 % Allowed : 27.31 % 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: -5.16 (0.32), residues: 240 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.93 (0.25), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS J 18 PHE 0.011 0.001 PHE J 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: 7 poor density : 12 time to evaluate : 0.322 Fit side-chains outliers start: 7 outliers final: 2 residues processed: 19 average time/residue: 0.0895 time to fit residues: 2.8307 Evaluate side-chains 14 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 12 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 29 SER Chi-restraints excluded: chain J residue 15 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 12 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 11 optimal weight: 0.0770 chunk 9 optimal weight: 2.9990 chunk 21 optimal weight: 0.1980 chunk 6 optimal weight: 2.9990 chunk 5 optimal weight: 0.5980 chunk 17 optimal weight: 0.6980 overall best weight: 0.4738 ------------------------------------------------------------------------------- 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** ** F 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4406 r_free = 0.4406 target = 0.101676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.094354 restraints weight = 20676.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.096737 restraints weight = 7376.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.098196 restraints weight = 3580.808| |-----------------------------------------------------------------------------| r_work (final): 0.4328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.5790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.010 2076 Z= 0.086 Angle : 0.455 3.819 2820 Z= 0.252 Chirality : 0.042 0.131 324 Planarity : 0.001 0.004 372 Dihedral : 6.212 25.951 348 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer: Outliers : 0.93 % Allowed : 25.93 % Favored : 73.15 % 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: -5.13 (0.33), residues: 240 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.90 (0.25), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS K 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 17 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 15 time to evaluate : 0.282 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 17 average time/residue: 0.1004 time to fit residues: 2.7465 Evaluate side-chains 15 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 14 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 15 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 7 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 23 optimal weight: 0.7980 chunk 1 optimal weight: 1.9990 chunk 5 optimal weight: 0.5980 chunk 19 optimal weight: 0.5980 chunk 22 optimal weight: 0.0980 chunk 12 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- 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 = 0.4380 r_free = 0.4380 target = 0.100111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.092845 restraints weight = 20853.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.095171 restraints weight = 7465.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.096591 restraints weight = 3638.778| |-----------------------------------------------------------------------------| r_work (final): 0.4298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.6076 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= 0.102 Angle : 0.466 4.071 2820 Z= 0.258 Chirality : 0.042 0.129 324 Planarity : 0.002 0.004 372 Dihedral : 6.261 25.228 348 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.58 % Favored : 90.42 % Rotamer: Outliers : 1.85 % Allowed : 25.93 % Favored : 72.22 % 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 0.004 0.002 HIS K 18 PHE 0.007 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 18 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 14 time to evaluate : 0.326 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 17 average time/residue: 0.1026 time to fit residues: 3.0373 Evaluate side-chains 17 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 14 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 36 THR Chi-restraints excluded: chain I residue 16 LEU Chi-restraints excluded: chain J residue 15 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 5 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 15 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 21 optimal weight: 0.5980 chunk 3 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.4333 r_free = 0.4333 target = 0.097544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.090418 restraints weight = 20960.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.092705 restraints weight = 7575.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.094100 restraints weight = 3691.929| |-----------------------------------------------------------------------------| r_work (final): 0.4251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.6295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.012 2076 Z= 0.124 Angle : 0.483 3.755 2820 Z= 0.270 Chirality : 0.042 0.128 324 Planarity : 0.002 0.004 372 Dihedral : 6.372 24.869 348 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 13.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.00 % Favored : 90.00 % Rotamer: Outliers : 1.85 % Allowed : 26.39 % Favored : 71.76 % 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: -5.30 (0.32), residues: 240 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.03 (0.25), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS G 18 PHE 0.006 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 19 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 15 time to evaluate : 0.324 Fit side-chains REVERT: I 15 PHE cc_start: 0.5560 (OUTLIER) cc_final: 0.3877 (m-80) outliers start: 4 outliers final: 3 residues processed: 18 average time/residue: 0.1137 time to fit residues: 3.2073 Evaluate side-chains 18 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 14 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 15 PHE Chi-restraints excluded: chain I residue 16 LEU Chi-restraints excluded: chain J residue 15 PHE 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: 1.9990 chunk 17 optimal weight: 2.9990 chunk 13 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 23 optimal weight: 0.5980 chunk 16 optimal weight: 0.7980 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 = 0.4333 r_free = 0.4333 target = 0.097436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.090340 restraints weight = 21081.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.092646 restraints weight = 7596.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.094041 restraints weight = 3687.373| |-----------------------------------------------------------------------------| r_work (final): 0.4254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.6508 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= 0.112 Angle : 0.472 3.389 2820 Z= 0.264 Chirality : 0.042 0.125 324 Planarity : 0.002 0.004 372 Dihedral : 6.258 24.900 348 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 16.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.42 % Favored : 89.58 % Rotamer: Outliers : 2.31 % Allowed : 25.93 % Favored : 71.76 % 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 0.004 0.002 HIS K 18 PHE 0.006 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 19 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 14 time to evaluate : 0.419 Fit side-chains REVERT: I 15 PHE cc_start: 0.5656 (OUTLIER) cc_final: 0.3707 (m-80) outliers start: 5 outliers final: 4 residues processed: 18 average time/residue: 0.1168 time to fit residues: 3.3477 Evaluate side-chains 19 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 14 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 15 PHE Chi-restraints excluded: chain I residue 16 LEU Chi-restraints excluded: chain J residue 15 PHE Chi-restraints excluded: chain J residue 34 SER Chi-restraints excluded: chain K residue 36 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 23 optimal weight: 0.0070 chunk 0 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 20 optimal weight: 0.0980 chunk 7 optimal weight: 0.3980 chunk 2 optimal weight: 1.9990 chunk 3 optimal weight: 0.5980 chunk 19 optimal weight: 0.5980 chunk 8 optimal weight: 0.5980 chunk 4 optimal weight: 0.5980 overall best weight: 0.3398 ------------------------------------------------------------------------------- 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** ** E 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4399 r_free = 0.4399 target = 0.102159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.094938 restraints weight = 20158.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.097365 restraints weight = 7247.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.098815 restraints weight = 3464.153| |-----------------------------------------------------------------------------| r_work (final): 0.4325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.6585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.010 2076 Z= 0.075 Angle : 0.428 3.431 2820 Z= 0.239 Chirality : 0.042 0.124 324 Planarity : 0.001 0.004 372 Dihedral : 5.923 25.042 348 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 14.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 1.85 % Allowed : 25.93 % Favored : 72.22 % 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: -5.28 (0.33), residues: 240 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.02 (0.25), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS K 18 PHE 0.010 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 20 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 16 time to evaluate : 0.317 Fit side-chains REVERT: I 15 PHE cc_start: 0.5713 (OUTLIER) cc_final: 0.3623 (m-80) outliers start: 4 outliers final: 3 residues processed: 20 average time/residue: 0.1237 time to fit residues: 3.6626 Evaluate side-chains 18 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 14 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 15 PHE Chi-restraints excluded: chain I residue 16 LEU Chi-restraints excluded: chain J residue 15 PHE Chi-restraints excluded: chain J residue 34 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 9 optimal weight: 0.7980 chunk 0 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 21 optimal weight: 0.0770 chunk 2 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 5 optimal weight: 0.9980 overall best weight: 0.6938 ------------------------------------------------------------------------------- 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 = 0.4354 r_free = 0.4354 target = 0.098534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.091424 restraints weight = 20620.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.093765 restraints weight = 7485.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.095162 restraints weight = 3611.612| |-----------------------------------------------------------------------------| r_work (final): 0.4277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.6677 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= 0.105 Angle : 0.457 3.528 2820 Z= 0.256 Chirality : 0.042 0.125 324 Planarity : 0.002 0.004 372 Dihedral : 6.011 24.087 348 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 16.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.67 % Favored : 88.33 % Rotamer: Outliers : 1.85 % Allowed : 26.85 % Favored : 71.30 % 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: -5.37 (0.32), residues: 240 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.09 (0.25), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS K 18 PHE 0.006 0.001 PHE C 23 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2459.12 seconds wall clock time: 44 minutes 16.55 seconds (2656.55 seconds total)