Starting phenix.real_space_refine on Wed Jul 23 12:24:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8bdz_15995/07_2025/8bdz_15995.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bdz_15995/07_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_15995/07_2025/8bdz_15995.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bdz_15995/07_2025/8bdz_15995.map" model { file = "/net/cci-nas-00/data/ceres_data/8bdz_15995/07_2025/8bdz_15995.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bdz_15995/07_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-5711/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: 4.40, per 1000 atoms: 1.33 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: 0.88 Conformation dependent library (CDL) restraints added in 343.9 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: 0.30 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: 0.84 Time building geometry restraints manager: 1.05 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: 3.810 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: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 14.410 Find NCS groups from input model: 0.110 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:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.480 ------------------------------------------------------------------------------- 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 3412 Z= 0.111 Angle : 0.523 6.373 4664 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 Details of bonding type rmsd hydrogen bonds : bond 0.14253 ( 218) hydrogen bonds : angle 5.96385 ( 618) SS BOND : bond 0.00188 ( 1) SS BOND : angle 0.68347 ( 2) covalent geometry : bond 0.00227 ( 3411) covalent geometry : angle 0.52247 ( 4662) *********************** 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 : 0.485 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: 0.2564 time to fit residues: 12.7525 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 : 0.445 ------------------------------------------------------------------------------- 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 3412 Z= 0.185 Angle : 0.572 5.077 4664 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 Details of bonding type rmsd hydrogen bonds : bond 0.04672 ( 218) hydrogen bonds : angle 5.04160 ( 618) SS BOND : bond 0.00103 ( 1) SS BOND : angle 0.55294 ( 2) covalent geometry : bond 0.00425 ( 3411) covalent geometry : angle 0.57237 ( 4662) *********************** 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 : 0.416 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: 0.2061 time to fit residues: 8.3310 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 : 0.393 ------------------------------------------------------------------------------- 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 3412 Z= 0.206 Angle : 0.581 5.290 4664 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 Details of bonding type rmsd hydrogen bonds : bond 0.04376 ( 218) hydrogen bonds : angle 4.77521 ( 618) SS BOND : bond 0.00229 ( 1) SS BOND : angle 0.57353 ( 2) covalent geometry : bond 0.00478 ( 3411) covalent geometry : angle 0.58105 ( 4662) *********************** 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 : 0.600 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: 0.3115 time to fit residues: 12.3352 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 : 1.687 ------------------------------------------------------------------------------- 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: 0.9990 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: 0.9980 overall best weight: 2.9988 ------------------------------------------------------------------------------- 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 = 0.3411 r_free = 0.3411 target = 0.054888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.044581 restraints weight = 16575.054| |-----------------------------------------------------------------------------| r_work (start): 0.3058 rms_B_bonded: 2.78 r_work: 0.2951 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.1734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3412 Z= 0.148 Angle : 0.541 5.437 4664 Z= 0.284 Chirality : 0.038 0.115 525 Planarity : 0.005 0.041 585 Dihedral : 4.020 16.447 447 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.09 % Allowed : 11.20 % Favored : 87.70 % 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: 2.74 (0.42), residues: 402 helix: 1.87 (0.30), residues: 292 sheet: None (None), residues: 0 loop : 1.99 (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 0.008 0.001 TYR C 272 ARG 0.002 0.000 ARG C 26 Details of bonding type rmsd hydrogen bonds : bond 0.03996 ( 218) hydrogen bonds : angle 4.56170 ( 618) SS BOND : bond 0.00042 ( 1) SS BOND : angle 0.58269 ( 2) covalent geometry : bond 0.00338 ( 3411) covalent geometry : angle 0.54112 ( 4662) *********************** 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 32 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 28 time to evaluate : 0.415 Fit side-chains REVERT: C 233 MET cc_start: 0.8911 (mpp) cc_final: 0.8416 (mpp) outliers start: 4 outliers final: 2 residues processed: 31 average time/residue: 0.1930 time to fit residues: 7.4807 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 : 0.391 ------------------------------------------------------------------------------- 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: 7.9990 chunk 34 optimal weight: 7.9990 chunk 2 optimal weight: 0.9990 chunk 28 optimal weight: 4.9990 chunk 3 optimal weight: 7.9990 chunk 30 optimal weight: 5.9990 chunk 19 optimal weight: 3.9990 chunk 6 optimal weight: 5.9990 chunk 12 optimal weight: 1.9990 chunk 26 optimal weight: 10.0000 overall best weight: 3.5990 ------------------------------------------------------------------------------- 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 = 0.054623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.044310 restraints weight = 16299.619| |-----------------------------------------------------------------------------| r_work (start): 0.3053 rms_B_bonded: 2.78 r_work: 0.2947 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.1825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 3412 Z= 0.168 Angle : 0.553 5.480 4664 Z= 0.291 Chirality : 0.038 0.120 525 Planarity : 0.005 0.039 585 Dihedral : 4.032 16.743 447 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % 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: 2.73 (0.42), residues: 402 helix: 1.87 (0.30), residues: 292 sheet: None (None), residues: 0 loop : 1.96 (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 0.016 0.001 PHE B 237 TYR 0.009 0.001 TYR C 272 ARG 0.001 0.000 ARG B 222 Details of bonding type rmsd hydrogen bonds : bond 0.03986 ( 218) hydrogen bonds : angle 4.54121 ( 618) SS BOND : bond 0.00108 ( 1) SS BOND : angle 0.64792 ( 2) covalent geometry : bond 0.00389 ( 3411) covalent geometry : angle 0.55322 ( 4662) *********************** 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 : 0.396 Fit side-chains REVERT: C 233 MET cc_start: 0.8919 (mpp) cc_final: 0.8451 (mpp) outliers start: 3 outliers final: 2 residues processed: 30 average time/residue: 0.1734 time to fit residues: 6.5464 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 : 0.375 ------------------------------------------------------------------------------- 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: 7.9990 chunk 31 optimal weight: 1.9990 chunk 23 optimal weight: 7.9990 chunk 36 optimal weight: 0.9980 chunk 37 optimal weight: 7.9990 chunk 20 optimal weight: 30.0000 chunk 34 optimal weight: 9.9990 chunk 25 optimal weight: 0.6980 chunk 8 optimal weight: 20.0000 chunk 38 optimal weight: 0.4980 chunk 26 optimal weight: 10.0000 overall best weight: 2.4384 ------------------------------------------------------------------------------- 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 = 0.054543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.044245 restraints weight = 16984.227| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 2.82 r_work: 0.2943 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.1842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3412 Z= 0.138 Angle : 0.563 7.064 4664 Z= 0.292 Chirality : 0.037 0.139 525 Planarity : 0.004 0.037 585 Dihedral : 3.962 16.392 447 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.64 % Allowed : 12.57 % 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: 2.87 (0.42), residues: 402 helix: 1.97 (0.30), residues: 292 sheet: None (None), residues: 0 loop : 2.01 (0.65), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 60 HIS 0.004 0.001 HIS A 244 PHE 0.012 0.001 PHE B 237 TYR 0.009 0.001 TYR B 228 ARG 0.002 0.000 ARG C 37 Details of bonding type rmsd hydrogen bonds : bond 0.03788 ( 218) hydrogen bonds : angle 4.39477 ( 618) SS BOND : bond 0.00010 ( 1) SS BOND : angle 0.73781 ( 2) covalent geometry : bond 0.00316 ( 3411) covalent geometry : angle 0.56332 ( 4662) *********************** 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 35 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 29 time to evaluate : 0.402 Fit side-chains REVERT: C 233 MET cc_start: 0.8880 (mpp) cc_final: 0.8516 (mpp) outliers start: 6 outliers final: 4 residues processed: 33 average time/residue: 0.1608 time to fit residues: 6.7655 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 : 0.400 ------------------------------------------------------------------------------- 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: 4.9990 chunk 4 optimal weight: 9.9990 chunk 21 optimal weight: 3.9990 chunk 38 optimal weight: 10.0000 chunk 1 optimal weight: 7.9990 chunk 15 optimal weight: 6.9990 chunk 20 optimal weight: 20.0000 chunk 6 optimal weight: 5.9990 chunk 7 optimal weight: 8.9990 chunk 0 optimal weight: 6.9990 chunk 25 optimal weight: 0.2980 overall best weight: 4.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 GLN B 230 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.054002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.043797 restraints weight = 16503.267| |-----------------------------------------------------------------------------| r_work (start): 0.3036 rms_B_bonded: 2.73 r_work: 0.2925 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.2030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 3412 Z= 0.195 Angle : 0.593 6.611 4664 Z= 0.308 Chirality : 0.039 0.139 525 Planarity : 0.005 0.038 585 Dihedral : 4.020 17.153 447 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % 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: 2.74 (0.42), residues: 402 helix: 1.90 (0.30), residues: 292 sheet: None (None), residues: 0 loop : 1.90 (0.63), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 60 HIS 0.005 0.001 HIS A 244 PHE 0.012 0.001 PHE B 237 TYR 0.010 0.002 TYR C 272 ARG 0.002 0.000 ARG B 238 Details of bonding type rmsd hydrogen bonds : bond 0.04024 ( 218) hydrogen bonds : angle 4.49246 ( 618) SS BOND : bond 0.00214 ( 1) SS BOND : angle 0.68105 ( 2) covalent geometry : bond 0.00457 ( 3411) covalent geometry : angle 0.59291 ( 4662) *********************** 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 : 0.402 Fit side-chains REVERT: C 233 MET cc_start: 0.8890 (mpp) cc_final: 0.8465 (mpp) outliers start: 7 outliers final: 5 residues processed: 33 average time/residue: 0.1678 time to fit residues: 7.0718 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 : 0.405 ------------------------------------------------------------------------------- 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 31 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 16 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 11 optimal weight: 3.9990 chunk 34 optimal weight: 0.0370 chunk 25 optimal weight: 0.0020 chunk 9 optimal weight: 0.9990 chunk 30 optimal weight: 9.9990 chunk 35 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 20 optimal weight: 50.0000 chunk 26 optimal weight: 7.9990 overall best weight: 0.6070 ------------------------------------------------------------------------------- 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 = 0.3432 r_free = 0.3432 target = 0.055568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.045275 restraints weight = 16406.594| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 2.81 r_work: 0.2979 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.2010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 3412 Z= 0.112 Angle : 0.559 6.660 4664 Z= 0.288 Chirality : 0.035 0.126 525 Planarity : 0.004 0.033 585 Dihedral : 3.884 15.445 447 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.37 % Allowed : 12.02 % 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: 2.97 (0.43), residues: 402 helix: 2.12 (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 0.009 0.001 TYR A 228 ARG 0.001 0.000 ARG A 37 Details of bonding type rmsd hydrogen bonds : bond 0.03542 ( 218) hydrogen bonds : angle 4.14837 ( 618) SS BOND : bond 0.00107 ( 1) SS BOND : angle 0.66187 ( 2) covalent geometry : bond 0.00243 ( 3411) covalent geometry : angle 0.55857 ( 4662) *********************** 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 36 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 31 time to evaluate : 0.395 Fit side-chains REVERT: A 233 MET cc_start: 0.8309 (mtp) cc_final: 0.8082 (mtm) REVERT: C 44 GLU cc_start: 0.7795 (OUTLIER) cc_final: 0.7517 (pp20) REVERT: C 233 MET cc_start: 0.8832 (mpp) cc_final: 0.8506 (mpp) outliers start: 5 outliers final: 4 residues processed: 33 average time/residue: 0.2091 time to fit residues: 8.3382 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 : 0.415 ------------------------------------------------------------------------------- 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: 10.0000 chunk 29 optimal weight: 6.9990 chunk 20 optimal weight: 20.0000 chunk 34 optimal weight: 7.9990 chunk 27 optimal weight: 9.9990 chunk 30 optimal weight: 10.0000 chunk 9 optimal weight: 0.9990 chunk 35 optimal weight: 0.7980 chunk 31 optimal weight: 3.9990 chunk 33 optimal weight: 10.0000 chunk 11 optimal weight: 0.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- 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 = 0.3404 r_free = 0.3404 target = 0.054692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.044451 restraints weight = 16674.162| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 2.75 r_work: 0.2952 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.2083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 3412 Z= 0.153 Angle : 0.609 7.377 4664 Z= 0.317 Chirality : 0.037 0.131 525 Planarity : 0.005 0.049 585 Dihedral : 3.858 15.538 447 Min Nonbonded Distance : 2.506 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: 2.92 (0.43), residues: 402 helix: 2.08 (0.31), residues: 290 sheet: None (None), residues: 0 loop : 1.82 (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 0.012 0.001 PHE B 237 TYR 0.009 0.001 TYR C 272 ARG 0.008 0.000 ARG C 252 Details of bonding type rmsd hydrogen bonds : bond 0.03718 ( 218) hydrogen bonds : angle 4.27206 ( 618) SS BOND : bond 0.00064 ( 1) SS BOND : angle 0.72741 ( 2) covalent geometry : bond 0.00361 ( 3411) covalent geometry : angle 0.60908 ( 4662) *********************** 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 33 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 28 time to evaluate : 0.496 Fit side-chains REVERT: C 44 GLU cc_start: 0.7817 (OUTLIER) cc_final: 0.7556 (pp20) REVERT: C 233 MET cc_start: 0.8840 (mpp) cc_final: 0.8510 (mpp) outliers start: 5 outliers final: 4 residues processed: 30 average time/residue: 0.1849 time to fit residues: 7.1715 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 : 0.439 ------------------------------------------------------------------------------- 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: 0.9980 chunk 23 optimal weight: 0.9980 chunk 20 optimal weight: 50.0000 chunk 38 optimal weight: 0.0980 chunk 34 optimal weight: 10.0000 chunk 30 optimal weight: 6.9990 chunk 6 optimal weight: 9.9990 chunk 8 optimal weight: 0.8980 chunk 33 optimal weight: 0.0980 chunk 16 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3436 r_free = 0.3436 target = 0.055787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.045587 restraints weight = 16290.141| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 2.77 r_work: 0.2996 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.2082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3412 Z= 0.118 Angle : 0.592 7.467 4664 Z= 0.309 Chirality : 0.036 0.128 525 Planarity : 0.005 0.037 585 Dihedral : 3.823 14.684 447 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.64 % Allowed : 13.11 % 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: 2.86 (0.43), residues: 402 helix: 2.02 (0.31), residues: 290 sheet: None (None), residues: 0 loop : 1.85 (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 0.010 0.001 PHE B 237 TYR 0.009 0.001 TYR A 228 ARG 0.007 0.000 ARG C 252 Details of bonding type rmsd hydrogen bonds : bond 0.03499 ( 218) hydrogen bonds : angle 4.12565 ( 618) SS BOND : bond 0.00101 ( 1) SS BOND : angle 0.64828 ( 2) covalent geometry : bond 0.00264 ( 3411) covalent geometry : angle 0.59208 ( 4662) ********************** 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 37 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 31 time to evaluate : 0.431 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 44 GLU cc_start: 0.7772 (OUTLIER) cc_final: 0.7522 (pp20) REVERT: C 233 MET cc_start: 0.8747 (mpp) cc_final: 0.8506 (mpp) outliers start: 6 outliers final: 5 residues processed: 34 average time/residue: 0.2427 time to fit residues: 9.8644 Evaluate side-chains 36 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 30 time to evaluate : 0.438 ------------------------------------------------------------------------------- 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 14 LEU 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: 0.0980 chunk 28 optimal weight: 0.9980 chunk 5 optimal weight: 6.9990 chunk 10 optimal weight: 9.9990 chunk 27 optimal weight: 4.9990 chunk 23 optimal weight: 0.9980 chunk 34 optimal weight: 8.9990 chunk 25 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- 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 = 0.3421 r_free = 0.3421 target = 0.055346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.045206 restraints weight = 16538.818| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 2.76 r_work: 0.2980 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.2106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3412 Z= 0.128 Angle : 0.611 7.690 4664 Z= 0.319 Chirality : 0.036 0.128 525 Planarity : 0.004 0.035 585 Dihedral : 3.766 14.408 447 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.64 % Allowed : 13.39 % 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: 2.87 (0.43), residues: 402 helix: 2.03 (0.31), residues: 290 sheet: None (None), residues: 0 loop : 1.86 (0.65), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 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 Details of bonding type rmsd hydrogen bonds : bond 0.03513 ( 218) hydrogen bonds : angle 4.13996 ( 618) SS BOND : bond 0.00042 ( 1) SS BOND : angle 0.66767 ( 2) covalent geometry : bond 0.00301 ( 3411) covalent geometry : angle 0.61113 ( 4662) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2185.77 seconds wall clock time: 39 minutes 22.36 seconds (2362.36 seconds total)