Starting phenix.real_space_refine on Wed Mar 5 18:37:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8bdz_15995/03_2025/8bdz_15995.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bdz_15995/03_2025/8bdz_15995.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.13 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8bdz_15995/03_2025/8bdz_15995.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bdz_15995/03_2025/8bdz_15995.map" model { file = "/net/cci-nas-00/data/ceres_data/8bdz_15995/03_2025/8bdz_15995.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bdz_15995/03_2025/8bdz_15995.cif" } resolution = 3.13 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= 0.063 sd= 0.372 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 18 5.16 5 C 2157 2.51 5 N 546 2.21 5 O 588 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 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: 3309 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1103 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 11, 'TRANS': 126} Chain breaks: 1 Chain: "B" Number of atoms: 1103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1103 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 11, 'TRANS': 126} Chain breaks: 1 Chain: "C" Number of atoms: 1103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1103 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 11, 'TRANS': 126} Chain breaks: 1 Time building chain proxies: 3.96, per 1000 atoms: 1.20 Number of scatterers: 3309 At special positions: 0 Unit cell: (87.4532, 76.3832, 91.8812, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 18 16.00 O 588 8.00 N 546 7.00 C 2157 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 59 " - pdb=" SG CYS B 59 " distance=2.03 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: 0.75 Conformation dependent library (CDL) restraints added in 359.2 milliseconds 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 786 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 0 sheets defined 82.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'A' and resid 4 through 8 removed outlier: 3.600A pdb=" N GLY A 8 " --> pdb=" O LYS A 5 " (cutoff:3.500A) Processing helix chain 'A' and resid 10 through 15 Processing helix chain 'A' and resid 16 through 17 No H-bonds generated for 'chain 'A' and resid 16 through 17' Processing helix chain 'A' and resid 18 through 22 removed outlier: 3.724A pdb=" N PHE A 22 " --> pdb=" O SER A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 24 through 41 removed outlier: 3.911A pdb=" N ARG A 37 " --> pdb=" O SER A 33 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N GLU A 38 " --> pdb=" O ALA A 34 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N ALA A 39 " --> pdb=" O LEU A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 73 removed outlier: 3.604A pdb=" N THR A 51 " --> pdb=" O SER A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 232 removed outlier: 3.918A pdb=" N ASN A 230 " --> pdb=" O VAL A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 251 Processing helix chain 'A' and resid 251 through 268 Processing helix chain 'B' and resid 4 through 8 Processing helix chain 'B' and resid 10 through 16 removed outlier: 3.606A pdb=" N PHE B 16 " --> pdb=" O GLU B 12 " (cutoff:3.500A) Processing helix chain 'B' and resid 17 through 22 removed outlier: 6.296A pdb=" N ASP B 20 " --> pdb=" O LEU B 17 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N PHE B 22 " --> pdb=" O SER B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 41 removed outlier: 3.784A pdb=" N ARG B 37 " --> pdb=" O SER B 33 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N GLU B 38 " --> pdb=" O ALA B 34 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N ALA B 39 " --> pdb=" O LEU B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 72 removed outlier: 3.530A pdb=" N THR B 51 " --> pdb=" O SER B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 232 removed outlier: 3.837A pdb=" N VAL B 226 " --> pdb=" O ARG B 222 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N SER B 227 " --> pdb=" O ASP B 223 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ASN B 230 " --> pdb=" O VAL B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 251 Processing helix chain 'B' and resid 251 through 268 Processing helix chain 'B' and resid 269 through 273 Processing helix chain 'C' and resid 4 through 8 Processing helix chain 'C' and resid 10 through 16 removed outlier: 3.891A pdb=" N PHE C 16 " --> pdb=" O GLU C 12 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 22 removed outlier: 6.033A pdb=" N ASP C 20 " --> pdb=" O LEU C 17 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N PHE C 22 " --> pdb=" O SER C 19 " (cutoff:3.500A) Processing helix chain 'C' and resid 24 through 42 removed outlier: 3.875A pdb=" N ARG C 37 " --> pdb=" O SER C 33 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N GLU C 38 " --> pdb=" O ALA C 34 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N ALA C 39 " --> pdb=" O LEU C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 73 Processing helix chain 'C' and resid 222 through 230 removed outlier: 4.111A pdb=" N VAL C 226 " --> pdb=" O ARG C 222 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N SER C 227 " --> pdb=" O ASP C 223 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 251 removed outlier: 3.789A pdb=" N LYS C 236 " --> pdb=" O ASN C 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 268 Processing helix chain 'C' and resid 269 through 273 218 hydrogen bonds defined for protein. 618 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.87 Time building geometry restraints manager: 0.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 1032 1.35 - 1.46: 865 1.46 - 1.58: 1487 1.58 - 1.70: 0 1.70 - 1.81: 27 Bond restraints: 3411 Sorted by residual: bond pdb=" CD GLU A 257 " pdb=" OE1 GLU A 257 " ideal model delta sigma weight residual 1.249 1.232 0.017 1.90e-02 2.77e+03 8.33e-01 bond pdb=" CD GLU C 257 " pdb=" OE1 GLU C 257 " ideal model delta sigma weight residual 1.249 1.233 0.016 1.90e-02 2.77e+03 7.43e-01 bond pdb=" CD GLU B 257 " pdb=" OE1 GLU B 257 " ideal model delta sigma weight residual 1.249 1.234 0.015 1.90e-02 2.77e+03 6.64e-01 bond pdb=" CA CYS B 46 " pdb=" CB CYS B 46 " ideal model delta sigma weight residual 1.530 1.543 -0.013 1.69e-02 3.50e+03 5.91e-01 bond pdb=" CB GLU A 257 " pdb=" CG GLU A 257 " ideal model delta sigma weight residual 1.520 1.542 -0.022 3.00e-02 1.11e+03 5.34e-01 ... (remaining 3406 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.27: 4520 1.27 - 2.55: 103 2.55 - 3.82: 32 3.82 - 5.10: 6 5.10 - 6.37: 1 Bond angle restraints: 4662 Sorted by residual: angle pdb=" C HIS B 45 " pdb=" N CYS B 46 " pdb=" CA CYS B 46 " ideal model delta sigma weight residual 121.54 127.91 -6.37 1.91e+00 2.74e-01 1.11e+01 angle pdb=" N GLU A 257 " pdb=" CA GLU A 257 " pdb=" CB GLU A 257 " ideal model delta sigma weight residual 110.39 114.79 -4.40 1.66e+00 3.63e-01 7.02e+00 angle pdb=" C HIS C 45 " pdb=" N CYS C 46 " pdb=" CA CYS C 46 " ideal model delta sigma weight residual 121.54 126.54 -5.00 1.91e+00 2.74e-01 6.86e+00 angle pdb=" N GLU B 257 " pdb=" CA GLU B 257 " pdb=" CB GLU B 257 " ideal model delta sigma weight residual 110.28 114.08 -3.80 1.55e+00 4.16e-01 6.00e+00 angle pdb=" C ILE A 256 " pdb=" N GLU A 257 " pdb=" CA GLU A 257 " ideal model delta sigma weight residual 120.72 116.80 3.92 1.67e+00 3.59e-01 5.51e+00 ... (remaining 4657 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.27: 1722 12.27 - 24.53: 194 24.53 - 36.80: 61 36.80 - 49.06: 18 49.06 - 61.32: 6 Dihedral angle restraints: 2001 sinusoidal: 792 harmonic: 1209 Sorted by residual: dihedral pdb=" CA ASP A 2 " pdb=" CB ASP A 2 " pdb=" CG ASP A 2 " pdb=" OD1 ASP A 2 " ideal model delta sinusoidal sigma weight residual -30.00 -87.40 57.40 1 2.00e+01 2.50e-03 1.11e+01 dihedral pdb=" CB CYS A 59 " pdb=" SG CYS A 59 " pdb=" SG CYS B 59 " pdb=" CB CYS B 59 " ideal model delta sinusoidal sigma weight residual 93.00 118.39 -25.39 1 1.00e+01 1.00e-02 9.27e+00 dihedral pdb=" CA SER A 47 " pdb=" C SER A 47 " pdb=" N PRO A 48 " pdb=" CA PRO A 48 " ideal model delta harmonic sigma weight residual 180.00 165.01 14.99 0 5.00e+00 4.00e-02 8.99e+00 ... (remaining 1998 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 395 0.037 - 0.074: 104 0.074 - 0.112: 22 0.112 - 0.149: 2 0.149 - 0.186: 2 Chirality restraints: 525 Sorted by residual: chirality pdb=" CA GLU A 257 " pdb=" N GLU A 257 " pdb=" C GLU A 257 " pdb=" CB GLU A 257 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.65e-01 chirality pdb=" CA GLU C 257 " pdb=" N GLU C 257 " pdb=" C GLU C 257 " pdb=" CB GLU C 257 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.17e-01 chirality pdb=" CA GLU B 257 " pdb=" N GLU B 257 " pdb=" C GLU B 257 " pdb=" CB GLU B 257 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.52e-01 ... (remaining 522 not shown) Planarity restraints: 585 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU B 253 " 0.008 2.00e-02 2.50e+03 1.61e-02 2.59e+00 pdb=" C GLU B 253 " -0.028 2.00e-02 2.50e+03 pdb=" O GLU B 253 " 0.010 2.00e-02 2.50e+03 pdb=" N THR B 254 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR C 268 " 0.022 5.00e-02 4.00e+02 3.30e-02 1.74e+00 pdb=" N PRO C 269 " -0.057 5.00e-02 4.00e+02 pdb=" CA PRO C 269 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO C 269 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA HIS C 45 " 0.006 2.00e-02 2.50e+03 1.31e-02 1.71e+00 pdb=" C HIS C 45 " -0.023 2.00e-02 2.50e+03 pdb=" O HIS C 45 " 0.008 2.00e-02 2.50e+03 pdb=" N CYS C 46 " 0.008 2.00e-02 2.50e+03 ... (remaining 582 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 825 2.79 - 3.32: 3428 3.32 - 3.85: 5678 3.85 - 4.37: 6494 4.37 - 4.90: 11051 Nonbonded interactions: 27476 Sorted by model distance: nonbonded pdb=" OG SER C 47 " pdb=" ND1 HIS C 50 " model vdw 2.264 3.120 nonbonded pdb=" OG SER B 47 " pdb=" ND1 HIS B 50 " model vdw 2.300 3.120 nonbonded pdb=" O PHE A 22 " pdb=" NH2 ARG A 238 " model vdw 2.301 3.120 nonbonded pdb=" O GLU A 62 " pdb=" OG1 THR A 65 " model vdw 2.302 3.040 nonbonded pdb=" OE2 GLU A 62 " pdb=" NZ LYS B 236 " model vdw 2.319 3.120 ... (remaining 27471 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 13.850 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 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:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 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 : 0.002 0.022 3411 Z= 0.142 Angle : 0.522 6.373 4662 Z= 0.279 Chirality : 0.037 0.186 525 Planarity : 0.004 0.033 585 Dihedral : 12.414 61.325 1212 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.26 (0.43), residues: 402 helix: 1.50 (0.31), residues: 291 sheet: None (None), residues: 0 loop : 1.86 (0.65), residues: 111 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 265 HIS 0.003 0.001 HIS B 45 PHE 0.007 0.001 PHE A 237 TYR 0.006 0.001 TYR A 258 ARG 0.002 0.000 ARG A 37 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.365 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 5 LYS cc_start: 0.7412 (tmtt) cc_final: 0.6803 (tmtt) REVERT: C 233 MET cc_start: 0.8428 (mpp) cc_final: 0.7894 (mpp) outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.2240 time to fit residues: 11.0970 Evaluate side-chains 28 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 32 optimal weight: 10.0000 chunk 29 optimal weight: 9.9990 chunk 16 optimal weight: 9.9990 chunk 10 optimal weight: 7.9990 chunk 19 optimal weight: 5.9990 chunk 15 optimal weight: 5.9990 chunk 30 optimal weight: 9.9990 chunk 11 optimal weight: 5.9990 chunk 18 optimal weight: 0.8980 chunk 22 optimal weight: 0.9980 chunk 35 optimal weight: 10.0000 overall best weight: 3.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.054914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.044746 restraints weight = 16480.775| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 2.76 r_work: 0.2956 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.1134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 3411 Z= 0.271 Angle : 0.572 5.077 4662 Z= 0.302 Chirality : 0.040 0.147 525 Planarity : 0.005 0.040 585 Dihedral : 3.958 14.855 447 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.09 % Allowed : 6.83 % Favored : 92.08 % 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: 2.50 (0.42), residues: 402 helix: 1.69 (0.30), residues: 291 sheet: None (None), residues: 0 loop : 1.91 (0.62), residues: 111 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 60 HIS 0.005 0.001 HIS A 244 PHE 0.007 0.001 PHE B 237 TYR 0.009 0.001 TYR C 272 ARG 0.003 0.000 ARG B 238 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 31 time to evaluate : 0.343 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 233 MET cc_start: 0.8891 (mpp) cc_final: 0.8352 (mpp) outliers start: 4 outliers final: 4 residues processed: 33 average time/residue: 0.1853 time to fit residues: 7.4737 Evaluate side-chains 33 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 29 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 GLU Chi-restraints excluded: chain B residue 45 HIS Chi-restraints excluded: chain B residue 257 GLU Chi-restraints excluded: chain C residue 20 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 27 optimal weight: 9.9990 chunk 30 optimal weight: 10.0000 chunk 31 optimal weight: 0.8980 chunk 10 optimal weight: 7.9990 chunk 11 optimal weight: 3.9990 chunk 15 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 35 optimal weight: 8.9990 chunk 5 optimal weight: 7.9990 chunk 12 optimal weight: 20.0000 chunk 23 optimal weight: 4.9990 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 230 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.054527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.044220 restraints weight = 16138.180| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 2.73 r_work: 0.2943 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.1590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 3411 Z= 0.307 Angle : 0.581 5.290 4662 Z= 0.307 Chirality : 0.041 0.132 525 Planarity : 0.005 0.045 585 Dihedral : 4.079 16.527 447 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 1.64 % Allowed : 9.84 % Favored : 88.52 % 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: 2.57 (0.42), residues: 402 helix: 1.75 (0.30), residues: 292 sheet: None (None), residues: 0 loop : 1.92 (0.64), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 60 HIS 0.005 0.001 HIS A 244 PHE 0.008 0.001 PHE B 22 TYR 0.009 0.002 TYR C 272 ARG 0.002 0.000 ARG C 37 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 27 time to evaluate : 0.385 Fit side-chains REVERT: C 233 MET cc_start: 0.8921 (mpp) cc_final: 0.8391 (mpp) outliers start: 6 outliers final: 2 residues processed: 30 average time/residue: 0.1706 time to fit residues: 6.5149 Evaluate side-chains 29 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 27 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 GLU Chi-restraints excluded: chain B residue 45 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 21 optimal weight: 4.9990 chunk 8 optimal weight: 8.9990 chunk 18 optimal weight: 7.9990 chunk 34 optimal weight: 4.9990 chunk 36 optimal weight: 8.9990 chunk 38 optimal weight: 7.9990 chunk 20 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 3 optimal weight: 6.9990 chunk 0 optimal weight: 9.9990 chunk 10 optimal weight: 2.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 45 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.054516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.044188 restraints weight = 16628.097| |-----------------------------------------------------------------------------| r_work (start): 0.3042 rms_B_bonded: 2.78 r_work: 0.2935 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.1811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 3411 Z= 0.276 Angle : 0.560 5.388 4662 Z= 0.294 Chirality : 0.039 0.116 525 Planarity : 0.005 0.043 585 Dihedral : 4.083 17.157 447 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.09 % Allowed : 12.84 % Favored : 86.07 % 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: 2.66 (0.42), residues: 402 helix: 1.82 (0.30), residues: 292 sheet: None (None), residues: 0 loop : 1.92 (0.64), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 60 HIS 0.004 0.001 HIS A 244 PHE 0.007 0.001 PHE C 16 TYR 0.009 0.001 TYR C 272 ARG 0.002 0.000 ARG C 37 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 29 time to evaluate : 0.363 Fit side-chains REVERT: C 233 MET cc_start: 0.8951 (mpp) cc_final: 0.8421 (mpp) outliers start: 4 outliers final: 2 residues processed: 32 average time/residue: 0.1758 time to fit residues: 6.9705 Evaluate side-chains 30 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 28 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 GLU Chi-restraints excluded: chain B residue 45 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 20 optimal weight: 50.0000 chunk 21 optimal weight: 5.9990 chunk 34 optimal weight: 5.9990 chunk 2 optimal weight: 0.2980 chunk 28 optimal weight: 4.9990 chunk 3 optimal weight: 10.0000 chunk 30 optimal weight: 10.0000 chunk 19 optimal weight: 0.9990 chunk 6 optimal weight: 5.9990 chunk 12 optimal weight: 0.0070 chunk 26 optimal weight: 7.9990 overall best weight: 2.4604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.054670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.044388 restraints weight = 16256.175| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 2.76 r_work: 0.2952 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.1829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3411 Z= 0.205 Angle : 0.541 5.510 4662 Z= 0.285 Chirality : 0.037 0.117 525 Planarity : 0.005 0.039 585 Dihedral : 4.032 16.867 447 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 0.82 % Allowed : 13.11 % Favored : 86.07 % 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: 2.76 (0.42), residues: 402 helix: 1.90 (0.30), residues: 292 sheet: None (None), residues: 0 loop : 1.97 (0.64), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 60 HIS 0.004 0.001 HIS A 244 PHE 0.014 0.001 PHE B 237 TYR 0.008 0.001 TYR B 228 ARG 0.001 0.000 ARG C 37 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 28 time to evaluate : 0.385 Fit side-chains REVERT: C 233 MET cc_start: 0.8923 (mpp) cc_final: 0.8454 (mpp) outliers start: 3 outliers final: 2 residues processed: 30 average time/residue: 0.1724 time to fit residues: 6.6179 Evaluate side-chains 30 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 28 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 GLU Chi-restraints excluded: chain B residue 45 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 6 optimal weight: 5.9990 chunk 31 optimal weight: 6.9990 chunk 23 optimal weight: 9.9990 chunk 36 optimal weight: 10.0000 chunk 37 optimal weight: 2.9990 chunk 20 optimal weight: 0.4980 chunk 34 optimal weight: 9.9990 chunk 25 optimal weight: 4.9990 chunk 8 optimal weight: 9.9990 chunk 38 optimal weight: 6.9990 chunk 26 optimal weight: 10.0000 overall best weight: 4.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.054077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.043712 restraints weight = 17038.874| |-----------------------------------------------------------------------------| r_work (start): 0.3028 rms_B_bonded: 2.76 r_work: 0.2919 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.1976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3411 Z= 0.288 Angle : 0.591 7.150 4662 Z= 0.307 Chirality : 0.039 0.143 525 Planarity : 0.005 0.040 585 Dihedral : 4.066 17.554 447 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.91 % Allowed : 12.02 % Favored : 86.07 % 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: 2.72 (0.42), residues: 402 helix: 1.89 (0.30), residues: 292 sheet: None (None), residues: 0 loop : 1.86 (0.63), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 60 HIS 0.005 0.001 HIS A 244 PHE 0.013 0.001 PHE B 237 TYR 0.010 0.002 TYR C 272 ARG 0.002 0.000 ARG C 37 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 27 time to evaluate : 0.354 Fit side-chains REVERT: C 233 MET cc_start: 0.8931 (mpp) cc_final: 0.8440 (mpp) outliers start: 7 outliers final: 4 residues processed: 32 average time/residue: 0.1563 time to fit residues: 6.3797 Evaluate side-chains 31 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 27 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 HIS Chi-restraints excluded: chain A residue 257 GLU Chi-restraints excluded: chain A residue 267 ARG Chi-restraints excluded: chain B residue 45 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 22 optimal weight: 3.9990 chunk 4 optimal weight: 8.9990 chunk 21 optimal weight: 5.9990 chunk 38 optimal weight: 9.9990 chunk 1 optimal weight: 6.9990 chunk 15 optimal weight: 8.9990 chunk 20 optimal weight: 40.0000 chunk 6 optimal weight: 5.9990 chunk 7 optimal weight: 10.0000 chunk 0 optimal weight: 4.9990 chunk 25 optimal weight: 0.9980 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 230 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.053880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.043526 restraints weight = 16566.680| |-----------------------------------------------------------------------------| r_work (start): 0.3021 rms_B_bonded: 2.76 r_work: 0.2910 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.2117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3411 Z= 0.291 Angle : 0.591 6.502 4662 Z= 0.306 Chirality : 0.039 0.142 525 Planarity : 0.005 0.040 585 Dihedral : 4.090 18.156 447 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.91 % Allowed : 11.48 % Favored : 86.61 % 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: 2.71 (0.42), residues: 402 helix: 1.91 (0.30), residues: 292 sheet: None (None), residues: 0 loop : 1.79 (0.63), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 60 HIS 0.004 0.001 HIS A 244 PHE 0.012 0.001 PHE B 237 TYR 0.009 0.002 TYR C 272 ARG 0.002 0.000 ARG C 252 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 28 time to evaluate : 0.396 Fit side-chains REVERT: C 44 GLU cc_start: 0.7859 (OUTLIER) cc_final: 0.7619 (pp20) REVERT: C 233 MET cc_start: 0.8960 (mpp) cc_final: 0.8441 (mpp) outliers start: 7 outliers final: 4 residues processed: 31 average time/residue: 0.1737 time to fit residues: 6.7806 Evaluate side-chains 33 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 28 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 HIS Chi-restraints excluded: chain A residue 257 GLU Chi-restraints excluded: chain A residue 267 ARG Chi-restraints excluded: chain B residue 45 HIS Chi-restraints excluded: chain C residue 44 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 16 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 11 optimal weight: 0.9980 chunk 34 optimal weight: 9.9990 chunk 25 optimal weight: 4.9990 chunk 9 optimal weight: 0.9980 chunk 30 optimal weight: 8.9990 chunk 35 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 chunk 20 optimal weight: 30.0000 chunk 26 optimal weight: 10.0000 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.054833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.044627 restraints weight = 16341.990| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 2.74 r_work: 0.2957 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.2056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3411 Z= 0.182 Angle : 0.575 6.613 4662 Z= 0.298 Chirality : 0.036 0.132 525 Planarity : 0.004 0.034 585 Dihedral : 3.963 17.070 447 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.37 % Allowed : 12.84 % Favored : 85.79 % 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: 2.95 (0.43), residues: 402 helix: 2.13 (0.31), residues: 290 sheet: None (None), residues: 0 loop : 1.76 (0.65), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 60 HIS 0.003 0.001 HIS A 244 PHE 0.011 0.001 PHE B 237 TYR 0.008 0.001 TYR B 228 ARG 0.002 0.000 ARG C 252 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 30 time to evaluate : 0.393 Fit side-chains REVERT: C 44 GLU cc_start: 0.7799 (OUTLIER) cc_final: 0.7543 (pp20) REVERT: C 233 MET cc_start: 0.8853 (mpp) cc_final: 0.8487 (mpp) outliers start: 5 outliers final: 4 residues processed: 32 average time/residue: 0.1942 time to fit residues: 7.6707 Evaluate side-chains 33 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 28 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 HIS Chi-restraints excluded: chain A residue 257 GLU Chi-restraints excluded: chain A residue 267 ARG Chi-restraints excluded: chain B residue 45 HIS Chi-restraints excluded: chain C residue 44 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 24 optimal weight: 0.9990 chunk 29 optimal weight: 3.9990 chunk 20 optimal weight: 6.9990 chunk 34 optimal weight: 8.9990 chunk 27 optimal weight: 2.9990 chunk 30 optimal weight: 7.9990 chunk 9 optimal weight: 1.9990 chunk 35 optimal weight: 5.9990 chunk 31 optimal weight: 3.9990 chunk 33 optimal weight: 20.0000 chunk 11 optimal weight: 0.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.054584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.044319 restraints weight = 16597.784| |-----------------------------------------------------------------------------| r_work (start): 0.3053 rms_B_bonded: 2.76 r_work: 0.2945 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.2092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3411 Z= 0.211 Angle : 0.583 7.188 4662 Z= 0.302 Chirality : 0.037 0.131 525 Planarity : 0.005 0.041 585 Dihedral : 3.898 16.469 447 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.37 % Allowed : 13.39 % Favored : 85.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.95 (0.43), residues: 402 helix: 2.13 (0.31), residues: 290 sheet: None (None), residues: 0 loop : 1.76 (0.65), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 60 HIS 0.004 0.001 HIS A 244 PHE 0.011 0.001 PHE B 237 TYR 0.008 0.001 TYR C 272 ARG 0.008 0.000 ARG C 252 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 29 time to evaluate : 0.365 Fit side-chains REVERT: C 44 GLU cc_start: 0.7831 (OUTLIER) cc_final: 0.7568 (pp20) REVERT: C 233 MET cc_start: 0.8855 (mpp) cc_final: 0.8484 (mpp) outliers start: 5 outliers final: 4 residues processed: 31 average time/residue: 0.1665 time to fit residues: 6.6273 Evaluate side-chains 33 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 28 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 HIS Chi-restraints excluded: chain A residue 257 GLU Chi-restraints excluded: chain A residue 267 ARG Chi-restraints excluded: chain B residue 45 HIS Chi-restraints excluded: chain C residue 44 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 28 optimal weight: 0.9990 chunk 23 optimal weight: 3.9990 chunk 20 optimal weight: 50.0000 chunk 38 optimal weight: 0.8980 chunk 34 optimal weight: 5.9990 chunk 30 optimal weight: 0.5980 chunk 6 optimal weight: 10.0000 chunk 8 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 5 optimal weight: 6.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.054831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.044682 restraints weight = 16422.680| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 2.75 r_work: 0.2960 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.2111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 3411 Z= 0.202 Angle : 0.590 7.306 4662 Z= 0.305 Chirality : 0.036 0.130 525 Planarity : 0.005 0.039 585 Dihedral : 3.853 15.906 447 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.37 % Allowed : 13.66 % Favored : 84.97 % 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: 2.99 (0.43), residues: 402 helix: 2.14 (0.31), residues: 290 sheet: None (None), residues: 0 loop : 1.81 (0.65), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 60 HIS 0.003 0.001 HIS A 244 PHE 0.011 0.001 PHE B 237 TYR 0.008 0.001 TYR B 228 ARG 0.008 0.000 ARG C 252 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 30 time to evaluate : 0.385 Fit side-chains REVERT: C 44 GLU cc_start: 0.7776 (OUTLIER) cc_final: 0.7511 (pp20) REVERT: C 233 MET cc_start: 0.8807 (mpp) cc_final: 0.8492 (mpp) outliers start: 5 outliers final: 4 residues processed: 32 average time/residue: 0.1680 time to fit residues: 6.8202 Evaluate side-chains 34 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 29 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 HIS Chi-restraints excluded: chain A residue 257 GLU Chi-restraints excluded: chain A residue 267 ARG Chi-restraints excluded: chain B residue 45 HIS Chi-restraints excluded: chain C residue 44 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 12 optimal weight: 0.0020 chunk 28 optimal weight: 0.9980 chunk 5 optimal weight: 6.9990 chunk 10 optimal weight: 10.0000 chunk 27 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 34 optimal weight: 9.9990 chunk 25 optimal weight: 5.9990 chunk 38 optimal weight: 0.8980 chunk 24 optimal weight: 0.9980 chunk 32 optimal weight: 5.9990 overall best weight: 1.3790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.055132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.044874 restraints weight = 16417.166| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 2.79 r_work: 0.2967 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.2116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3411 Z= 0.187 Angle : 0.589 7.547 4662 Z= 0.306 Chirality : 0.036 0.128 525 Planarity : 0.005 0.035 585 Dihedral : 3.812 15.481 447 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.37 % Allowed : 13.39 % Favored : 85.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.99 (0.43), residues: 402 helix: 2.13 (0.31), residues: 290 sheet: None (None), residues: 0 loop : 1.84 (0.65), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 60 HIS 0.003 0.001 HIS A 244 PHE 0.011 0.001 PHE B 237 TYR 0.008 0.001 TYR B 228 ARG 0.007 0.000 ARG C 252 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1832.69 seconds wall clock time: 32 minutes 21.63 seconds (1941.63 seconds total)