Starting phenix.real_space_refine on Wed Sep 17 03:31:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xrq_38610/09_2025/8xrq_38610.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xrq_38610/09_2025/8xrq_38610.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.19 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8xrq_38610/09_2025/8xrq_38610.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xrq_38610/09_2025/8xrq_38610.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8xrq_38610/09_2025/8xrq_38610.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xrq_38610/09_2025/8xrq_38610.map" } resolution = 4.19 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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 11 5.16 5 C 2053 2.51 5 N 537 2.21 5 O 609 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3210 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1462 Classifications: {'peptide': 180} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 170} Chain: "B" Number of atoms: 934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 934 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 5, 'TRANS': 115} Chain: "C" Number of atoms: 814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 814 Classifications: {'peptide': 106} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 98} Time building chain proxies: 1.04, per 1000 atoms: 0.32 Number of scatterers: 3210 At special positions: 0 Unit cell: (71.048, 84.744, 68.48, 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 11 16.00 O 609 8.00 N 537 7.00 C 2053 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 95 " distance=2.04 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 88 " 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: 0.25 Conformation dependent library (CDL) restraints added in 108.6 milliseconds Enol-peptide restraints added in 0.0 nanoseconds 802 Ramachandran restraints generated. 401 Oldfield, 0 Emsley, 401 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 746 Finding SS restraints... Secondary structure from input PDB file: 3 helices and 8 sheets defined 4.9% alpha, 19.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.11 Creating SS restraints... Processing helix chain 'A' and resid 365 through 371 removed outlier: 3.566A pdb=" N ASN A 370 " --> pdb=" O SER A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 411 removed outlier: 5.067A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 421 removed outlier: 3.524A pdb=" N TYR A 421 " --> pdb=" O ASN A 417 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 357 through 358 removed outlier: 3.704A pdb=" N ILE A 358 " --> pdb=" O VAL A 395 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 357 through 358 removed outlier: 3.704A pdb=" N ILE A 358 " --> pdb=" O VAL A 395 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 452 through 453 Processing sheet with id=AA4, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AA5, first strand: chain 'B' and resid 57 through 59 removed outlier: 3.877A pdb=" N ASN B 58 " --> pdb=" O TYR B 50 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N TYR B 50 " --> pdb=" O ASN B 58 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N TRP B 47 " --> pdb=" O ARG B 38 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N ARG B 38 " --> pdb=" O TRP B 47 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLY B 49 " --> pdb=" O TRP B 36 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N TRP B 34 " --> pdb=" O VAL B 51 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLN B 39 " --> pdb=" O VAL B 92 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N VAL B 92 " --> pdb=" O GLN B 39 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N CYS B 95 " --> pdb=" O TRP B 112 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N TRP B 112 " --> pdb=" O CYS B 95 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ARG B 97 " --> pdb=" O ASP B 110 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 68 through 69 Processing sheet with id=AA7, first strand: chain 'C' and resid 19 through 21 removed outlier: 4.247A pdb=" N ILE C 75 " --> pdb=" O ALA C 19 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N LEU C 21 " --> pdb=" O LEU C 73 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N LEU C 73 " --> pdb=" O LEU C 21 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 53 through 54 removed outlier: 3.687A pdb=" N ASN C 53 " --> pdb=" O TYR C 49 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N TRP C 35 " --> pdb=" O LEU C 47 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N TYR C 49 " --> pdb=" O LEU C 33 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N LEU C 33 " --> pdb=" O TYR C 49 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLN C 38 " --> pdb=" O VAL C 85 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N VAL C 85 " --> pdb=" O GLN C 38 " (cutoff:3.500A) 48 hydrogen bonds defined for protein. 105 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: 0.33 Time building geometry restraints manager: 0.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 984 1.34 - 1.46: 813 1.46 - 1.58: 1490 1.58 - 1.70: 2 1.70 - 1.82: 12 Bond restraints: 3301 Sorted by residual: bond pdb=" C PHE B 78 " pdb=" N SER B 79 " ideal model delta sigma weight residual 1.331 1.440 -0.110 1.41e-02 5.03e+03 6.06e+01 bond pdb=" C ILE B 29 " pdb=" N SER B 30 " ideal model delta sigma weight residual 1.332 1.419 -0.087 1.38e-02 5.25e+03 3.96e+01 bond pdb=" C MET B 117 " pdb=" N VAL B 118 " ideal model delta sigma weight residual 1.330 1.403 -0.073 1.21e-02 6.83e+03 3.67e+01 bond pdb=" C VAL B 118 " pdb=" N THR B 119 " ideal model delta sigma weight residual 1.331 1.260 0.071 1.23e-02 6.61e+03 3.32e+01 bond pdb=" C SER B 40 " pdb=" N PRO B 41 " ideal model delta sigma weight residual 1.331 1.388 -0.057 1.21e-02 6.83e+03 2.21e+01 ... (remaining 3296 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.08: 4337 2.08 - 4.16: 119 4.16 - 6.24: 27 6.24 - 8.32: 7 8.32 - 10.40: 2 Bond angle restraints: 4492 Sorted by residual: angle pdb=" C SER B 40 " pdb=" N PRO B 41 " pdb=" CA PRO B 41 " ideal model delta sigma weight residual 120.11 110.63 9.48 1.12e+00 7.97e-01 7.16e+01 angle pdb=" N SER B 62 " pdb=" CA SER B 62 " pdb=" C SER B 62 " ideal model delta sigma weight residual 111.14 104.25 6.89 1.08e+00 8.57e-01 4.07e+01 angle pdb=" CA PRO C 40 " pdb=" N PRO C 40 " pdb=" CD PRO C 40 " ideal model delta sigma weight residual 112.00 103.92 8.08 1.40e+00 5.10e-01 3.33e+01 angle pdb=" O PHE B 78 " pdb=" C PHE B 78 " pdb=" N SER B 79 " ideal model delta sigma weight residual 123.06 129.73 -6.67 1.20e+00 6.94e-01 3.09e+01 angle pdb=" CA PHE B 78 " pdb=" C PHE B 78 " pdb=" N SER B 79 " ideal model delta sigma weight residual 115.91 108.96 6.95 1.29e+00 6.01e-01 2.90e+01 ... (remaining 4487 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 1674 18.00 - 36.00: 197 36.00 - 54.00: 43 54.00 - 72.00: 6 72.00 - 89.99: 4 Dihedral angle restraints: 1924 sinusoidal: 746 harmonic: 1178 Sorted by residual: dihedral pdb=" CB CYS B 22 " pdb=" SG CYS B 22 " pdb=" SG CYS B 95 " pdb=" CB CYS B 95 " ideal model delta sinusoidal sigma weight residual 93.00 157.56 -64.56 1 1.00e+01 1.00e-02 5.48e+01 dihedral pdb=" CB CYS C 23 " pdb=" SG CYS C 23 " pdb=" SG CYS C 88 " pdb=" CB CYS C 88 " ideal model delta sinusoidal sigma weight residual -86.00 -135.81 49.81 1 1.00e+01 1.00e-02 3.40e+01 dihedral pdb=" CA ASP B 89 " pdb=" CB ASP B 89 " pdb=" CG ASP B 89 " pdb=" OD1 ASP B 89 " ideal model delta sinusoidal sigma weight residual -30.00 -89.16 59.16 1 2.00e+01 2.50e-03 1.17e+01 ... (remaining 1921 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 299 0.038 - 0.075: 121 0.075 - 0.113: 45 0.113 - 0.151: 9 0.151 - 0.188: 2 Chirality restraints: 476 Sorted by residual: chirality pdb=" CA VAL B 118 " pdb=" N VAL B 118 " pdb=" C VAL B 118 " pdb=" CB VAL B 118 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.19 2.00e-01 2.50e+01 8.86e-01 chirality pdb=" CA VAL A 511 " pdb=" N VAL A 511 " pdb=" C VAL A 511 " pdb=" CB VAL A 511 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 6.83e-01 chirality pdb=" CA VAL C 104 " pdb=" N VAL C 104 " pdb=" C VAL C 104 " pdb=" CB VAL C 104 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.13 2.00e-01 2.50e+01 4.49e-01 ... (remaining 473 not shown) Planarity restraints: 578 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER B 40 " 0.024 2.00e-02 2.50e+03 4.73e-02 2.24e+01 pdb=" C SER B 40 " -0.082 2.00e-02 2.50e+03 pdb=" O SER B 40 " 0.031 2.00e-02 2.50e+03 pdb=" N PRO B 41 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS C 39 " 0.068 5.00e-02 4.00e+02 9.81e-02 1.54e+01 pdb=" N PRO C 40 " -0.169 5.00e-02 4.00e+02 pdb=" CA PRO C 40 " 0.048 5.00e-02 4.00e+02 pdb=" CD PRO C 40 " 0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 29 " -0.018 2.00e-02 2.50e+03 3.75e-02 1.41e+01 pdb=" C ILE B 29 " 0.065 2.00e-02 2.50e+03 pdb=" O ILE B 29 " -0.026 2.00e-02 2.50e+03 pdb=" N SER B 30 " -0.021 2.00e-02 2.50e+03 ... (remaining 575 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 1157 2.84 - 3.35: 2737 3.35 - 3.87: 4951 3.87 - 4.38: 5461 4.38 - 4.90: 9458 Nonbonded interactions: 23764 Sorted by model distance: nonbonded pdb=" O THR A 430 " pdb=" OG1 THR A 430 " model vdw 2.322 3.040 nonbonded pdb=" OE1 GLN C 42 " pdb=" O ALA C 43 " model vdw 2.417 3.040 nonbonded pdb=" O SER A 438 " pdb=" OG SER A 438 " model vdw 2.442 3.040 nonbonded pdb=" O SER B 103 " pdb=" N TRP B 105 " model vdw 2.463 3.120 nonbonded pdb=" O SER A 496 " pdb=" OG SER A 496 " model vdw 2.463 3.040 ... (remaining 23759 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: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 4.820 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4714 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 : 0.006 0.110 3305 Z= 0.383 Angle : 0.868 10.399 4500 Z= 0.541 Chirality : 0.047 0.188 476 Planarity : 0.008 0.098 578 Dihedral : 15.749 89.994 1166 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.25 % Allowed : 10.97 % Favored : 88.78 % Rotamer: Outliers : 0.86 % Allowed : 22.86 % Favored : 76.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.50 (0.38), residues: 401 helix: -4.96 (0.50), residues: 6 sheet: -1.66 (0.62), residues: 78 loop : -2.69 (0.31), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 66 TYR 0.008 0.001 TYR B 32 PHE 0.018 0.001 PHE C 83 TRP 0.013 0.001 TRP C 35 HIS 0.001 0.001 HIS B 77 Details of bonding type rmsd covalent geometry : bond 0.00611 ( 3301) covalent geometry : angle 0.86693 ( 4492) SS BOND : bond 0.00377 ( 4) SS BOND : angle 1.32614 ( 8) hydrogen bonds : bond 0.25843 ( 45) hydrogen bonds : angle 12.80089 ( 105) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 802 Ramachandran restraints generated. 401 Oldfield, 0 Emsley, 401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 802 Ramachandran restraints generated. 401 Oldfield, 0 Emsley, 401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 61 time to evaluate : 0.099 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 489 TYR cc_start: 0.5626 (m-80) cc_final: 0.5294 (m-80) REVERT: B 5 GLN cc_start: 0.6697 (mp10) cc_final: 0.6452 (mp10) REVERT: B 36 TRP cc_start: 0.5921 (m100) cc_final: 0.5620 (m100) outliers start: 3 outliers final: 0 residues processed: 64 average time/residue: 0.0806 time to fit residues: 6.0577 Evaluate side-chains 58 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 24 optimal weight: 0.0770 chunk 26 optimal weight: 0.3980 chunk 2 optimal weight: 0.9980 chunk 16 optimal weight: 0.2980 chunk 32 optimal weight: 0.0050 chunk 31 optimal weight: 0.0970 chunk 25 optimal weight: 0.6980 chunk 19 optimal weight: 0.3980 chunk 30 optimal weight: 0.5980 chunk 22 optimal weight: 0.7980 chunk 37 optimal weight: 0.2980 overall best weight: 0.1550 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 354 ASN ** C 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4431 r_free = 0.4431 target = 0.197793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.183341 restraints weight = 7123.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.186955 restraints weight = 4644.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.189449 restraints weight = 3195.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.191332 restraints weight = 2301.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4378 r_free = 0.4378 target = 0.192658 restraints weight = 1711.993| |-----------------------------------------------------------------------------| r_work (final): 0.4376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4686 moved from start: 0.2490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 3305 Z= 0.137 Angle : 0.694 11.158 4500 Z= 0.352 Chirality : 0.047 0.268 476 Planarity : 0.006 0.076 578 Dihedral : 4.891 21.326 452 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.25 % Allowed : 12.97 % Favored : 86.78 % Rotamer: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.45 (0.39), residues: 401 helix: -3.22 (0.91), residues: 21 sheet: -1.71 (0.56), residues: 97 loop : -2.61 (0.33), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 45 TYR 0.033 0.002 TYR B 52 PHE 0.014 0.002 PHE B 78 TRP 0.011 0.002 TRP B 112 HIS 0.002 0.001 HIS C 91 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 3301) covalent geometry : angle 0.69331 ( 4492) SS BOND : bond 0.00511 ( 4) SS BOND : angle 1.12731 ( 8) hydrogen bonds : bond 0.03164 ( 45) hydrogen bonds : angle 9.12684 ( 105) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 802 Ramachandran restraints generated. 401 Oldfield, 0 Emsley, 401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 802 Ramachandran restraints generated. 401 Oldfield, 0 Emsley, 401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.071 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 458 LYS cc_start: 0.1641 (ttmt) cc_final: 0.1250 (tppt) outliers start: 0 outliers final: 0 residues processed: 58 average time/residue: 0.0781 time to fit residues: 5.4019 Evaluate side-chains 57 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 0.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 4 optimal weight: 0.3980 chunk 30 optimal weight: 0.0870 chunk 7 optimal weight: 0.7980 chunk 23 optimal weight: 0.8980 chunk 27 optimal weight: 0.8980 chunk 39 optimal weight: 0.8980 chunk 15 optimal weight: 0.0670 chunk 34 optimal weight: 0.5980 chunk 1 optimal weight: 0.0970 chunk 33 optimal weight: 0.0770 chunk 32 optimal weight: 0.8980 overall best weight: 0.1452 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4408 r_free = 0.4408 target = 0.196377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.181685 restraints weight = 6947.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.185176 restraints weight = 4596.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.187688 restraints weight = 3232.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.189454 restraints weight = 2360.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.190821 restraints weight = 1786.872| |-----------------------------------------------------------------------------| r_work (final): 0.4350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4758 moved from start: 0.3346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 3305 Z= 0.127 Angle : 0.624 6.270 4500 Z= 0.323 Chirality : 0.044 0.156 476 Planarity : 0.006 0.085 578 Dihedral : 4.711 16.330 452 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.25 % Allowed : 10.97 % Favored : 88.78 % Rotamer: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.29 (0.39), residues: 401 helix: -3.09 (0.91), residues: 21 sheet: -1.64 (0.55), residues: 97 loop : -2.47 (0.33), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 97 TYR 0.014 0.001 TYR B 52 PHE 0.028 0.002 PHE C 30 TRP 0.014 0.002 TRP B 34 HIS 0.001 0.001 HIS A 505 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 3301) covalent geometry : angle 0.62298 ( 4492) SS BOND : bond 0.00429 ( 4) SS BOND : angle 0.98769 ( 8) hydrogen bonds : bond 0.03014 ( 45) hydrogen bonds : angle 8.34921 ( 105) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 802 Ramachandran restraints generated. 401 Oldfield, 0 Emsley, 401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 802 Ramachandran restraints generated. 401 Oldfield, 0 Emsley, 401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 0.072 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 458 LYS cc_start: 0.1927 (ttmt) cc_final: 0.1647 (tppt) outliers start: 0 outliers final: 0 residues processed: 59 average time/residue: 0.0715 time to fit residues: 5.0161 Evaluate side-chains 58 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 27 optimal weight: 0.4980 chunk 21 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 2 optimal weight: 0.5980 chunk 17 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 36 optimal weight: 0.9990 chunk 37 optimal weight: 0.4980 chunk 0 optimal weight: 0.9990 chunk 5 optimal weight: 0.0670 chunk 9 optimal weight: 0.0870 overall best weight: 0.3496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 42 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.189829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.173518 restraints weight = 6772.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.177229 restraints weight = 4505.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.179853 restraints weight = 3191.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.181651 restraints weight = 2376.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.183052 restraints weight = 1847.124| |-----------------------------------------------------------------------------| r_work (final): 0.4249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4953 moved from start: 0.4726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 3305 Z= 0.205 Angle : 0.727 7.445 4500 Z= 0.385 Chirality : 0.049 0.256 476 Planarity : 0.007 0.085 578 Dihedral : 5.815 28.168 452 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.25 % Allowed : 14.71 % Favored : 85.04 % Rotamer: Outliers : 0.57 % Allowed : 2.29 % Favored : 97.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.25 (0.39), residues: 401 helix: -2.72 (0.83), residues: 27 sheet: -1.28 (0.59), residues: 91 loop : -2.59 (0.33), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 403 TYR 0.010 0.002 TYR B 52 PHE 0.031 0.003 PHE A 486 TRP 0.023 0.003 TRP C 35 HIS 0.004 0.002 HIS A 505 Details of bonding type rmsd covalent geometry : bond 0.00442 ( 3301) covalent geometry : angle 0.72042 ( 4492) SS BOND : bond 0.01190 ( 4) SS BOND : angle 2.35863 ( 8) hydrogen bonds : bond 0.03713 ( 45) hydrogen bonds : angle 9.07194 ( 105) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 802 Ramachandran restraints generated. 401 Oldfield, 0 Emsley, 401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 802 Ramachandran restraints generated. 401 Oldfield, 0 Emsley, 401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 56 time to evaluate : 0.123 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 112 TRP cc_start: 0.6510 (OUTLIER) cc_final: 0.6226 (m-10) REVERT: C 56 THR cc_start: 0.8686 (t) cc_final: 0.8370 (p) outliers start: 2 outliers final: 0 residues processed: 57 average time/residue: 0.0844 time to fit residues: 5.6257 Evaluate side-chains 56 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 55 time to evaluate : 0.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 35 optimal weight: 0.2980 chunk 1 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 32 optimal weight: 0.6980 chunk 0 optimal weight: 0.9980 chunk 9 optimal weight: 0.7980 chunk 23 optimal weight: 0.8980 chunk 30 optimal weight: 0.2980 chunk 6 optimal weight: 0.0980 chunk 38 optimal weight: 0.0980 chunk 15 optimal weight: 0.2980 overall best weight: 0.2180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.189632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.174257 restraints weight = 6918.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.177557 restraints weight = 4720.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.180081 restraints weight = 3409.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.181871 restraints weight = 2554.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.183218 restraints weight = 1973.823| |-----------------------------------------------------------------------------| r_work (final): 0.4242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4950 moved from start: 0.5178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 3305 Z= 0.136 Angle : 0.632 7.124 4500 Z= 0.328 Chirality : 0.045 0.176 476 Planarity : 0.006 0.084 578 Dihedral : 5.325 20.130 452 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.25 % Allowed : 12.72 % Favored : 87.03 % Rotamer: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.11 (0.39), residues: 401 helix: -2.52 (0.92), residues: 27 sheet: -1.02 (0.60), residues: 86 loop : -2.54 (0.33), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 97 TYR 0.013 0.001 TYR C 49 PHE 0.018 0.002 PHE A 486 TRP 0.024 0.002 TRP B 112 HIS 0.002 0.001 HIS C 91 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 3301) covalent geometry : angle 0.63033 ( 4492) SS BOND : bond 0.00435 ( 4) SS BOND : angle 1.31098 ( 8) hydrogen bonds : bond 0.02817 ( 45) hydrogen bonds : angle 8.16551 ( 105) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 802 Ramachandran restraints generated. 401 Oldfield, 0 Emsley, 401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 802 Ramachandran restraints generated. 401 Oldfield, 0 Emsley, 401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 0.122 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 465 GLU cc_start: 0.6067 (tt0) cc_final: 0.5807 (tt0) REVERT: C 56 THR cc_start: 0.8684 (t) cc_final: 0.8401 (p) outliers start: 0 outliers final: 0 residues processed: 60 average time/residue: 0.0743 time to fit residues: 5.3302 Evaluate side-chains 59 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 0.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 38 optimal weight: 0.0980 chunk 31 optimal weight: 0.2980 chunk 34 optimal weight: 0.9980 chunk 18 optimal weight: 0.4980 chunk 35 optimal weight: 0.0370 chunk 25 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 chunk 22 optimal weight: 0.1980 chunk 7 optimal weight: 0.7980 chunk 0 optimal weight: 0.9990 chunk 8 optimal weight: 0.9980 overall best weight: 0.2258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 42 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.187142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.172150 restraints weight = 6883.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.175479 restraints weight = 4678.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.177854 restraints weight = 3377.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.179341 restraints weight = 2535.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.180818 restraints weight = 2019.046| |-----------------------------------------------------------------------------| r_work (final): 0.4218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4985 moved from start: 0.5745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 3305 Z= 0.138 Angle : 0.627 6.024 4500 Z= 0.326 Chirality : 0.045 0.169 476 Planarity : 0.006 0.082 578 Dihedral : 5.367 22.347 452 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.25 % Allowed : 12.47 % Favored : 87.28 % Rotamer: Outliers : 0.29 % Allowed : 3.71 % Favored : 96.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.03 (0.39), residues: 401 helix: -2.57 (0.94), residues: 27 sheet: -0.99 (0.63), residues: 74 loop : -2.43 (0.33), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 403 TYR 0.014 0.001 TYR A 508 PHE 0.022 0.002 PHE A 486 TRP 0.013 0.002 TRP B 112 HIS 0.003 0.001 HIS C 91 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 3301) covalent geometry : angle 0.62581 ( 4492) SS BOND : bond 0.00366 ( 4) SS BOND : angle 1.20403 ( 8) hydrogen bonds : bond 0.03146 ( 45) hydrogen bonds : angle 8.16122 ( 105) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 802 Ramachandran restraints generated. 401 Oldfield, 0 Emsley, 401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 802 Ramachandran restraints generated. 401 Oldfield, 0 Emsley, 401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 62 time to evaluate : 0.073 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 465 GLU cc_start: 0.6157 (tt0) cc_final: 0.5825 (tt0) REVERT: B 45 LEU cc_start: 0.7742 (mt) cc_final: 0.7389 (mm) REVERT: B 58 ASN cc_start: 0.6912 (t0) cc_final: 0.6653 (t0) REVERT: C 56 THR cc_start: 0.8681 (t) cc_final: 0.8434 (p) outliers start: 1 outliers final: 0 residues processed: 62 average time/residue: 0.0766 time to fit residues: 5.7046 Evaluate side-chains 61 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 14 optimal weight: 0.4980 chunk 32 optimal weight: 0.3980 chunk 9 optimal weight: 0.5980 chunk 29 optimal weight: 0.0970 chunk 3 optimal weight: 0.8980 chunk 23 optimal weight: 0.7980 chunk 19 optimal weight: 0.3980 chunk 15 optimal weight: 0.5980 chunk 22 optimal weight: 0.7980 chunk 24 optimal weight: 0.2980 chunk 39 optimal weight: 0.9990 overall best weight: 0.3378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.186176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.170684 restraints weight = 7097.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.173986 restraints weight = 4859.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.176354 restraints weight = 3511.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.178127 restraints weight = 2640.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.179488 restraints weight = 2052.356| |-----------------------------------------------------------------------------| r_work (final): 0.4198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5043 moved from start: 0.6291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 3305 Z= 0.181 Angle : 0.706 6.134 4500 Z= 0.372 Chirality : 0.047 0.186 476 Planarity : 0.006 0.082 578 Dihedral : 6.027 25.431 452 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.25 % Allowed : 12.97 % Favored : 86.78 % Rotamer: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.23 (0.39), residues: 401 helix: -2.64 (0.98), residues: 27 sheet: -1.39 (0.61), residues: 79 loop : -2.51 (0.33), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 457 TYR 0.012 0.002 TYR A 473 PHE 0.029 0.002 PHE A 486 TRP 0.022 0.003 TRP B 112 HIS 0.008 0.002 HIS C 91 Details of bonding type rmsd covalent geometry : bond 0.00406 ( 3301) covalent geometry : angle 0.69939 ( 4492) SS BOND : bond 0.00596 ( 4) SS BOND : angle 2.45122 ( 8) hydrogen bonds : bond 0.03293 ( 45) hydrogen bonds : angle 8.19233 ( 105) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 802 Ramachandran restraints generated. 401 Oldfield, 0 Emsley, 401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 802 Ramachandran restraints generated. 401 Oldfield, 0 Emsley, 401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.100 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 489 TYR cc_start: 0.4257 (m-80) cc_final: 0.3841 (m-10) REVERT: B 45 LEU cc_start: 0.7711 (mt) cc_final: 0.7323 (mm) REVERT: C 56 THR cc_start: 0.8711 (t) cc_final: 0.8467 (p) outliers start: 0 outliers final: 0 residues processed: 64 average time/residue: 0.0870 time to fit residues: 6.5000 Evaluate side-chains 62 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 36 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 15 optimal weight: 0.0970 chunk 11 optimal weight: 0.9980 chunk 22 optimal weight: 0.9980 chunk 16 optimal weight: 0.0770 chunk 35 optimal weight: 0.6980 chunk 39 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 chunk 10 optimal weight: 0.2980 chunk 1 optimal weight: 0.6980 overall best weight: 0.3736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.183558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.168413 restraints weight = 6995.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.171491 restraints weight = 4839.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.173669 restraints weight = 3535.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.175365 restraints weight = 2706.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.176678 restraints weight = 2139.470| |-----------------------------------------------------------------------------| r_work (final): 0.4163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5087 moved from start: 0.6876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 3305 Z= 0.194 Angle : 0.721 6.221 4500 Z= 0.382 Chirality : 0.048 0.172 476 Planarity : 0.007 0.082 578 Dihedral : 6.276 26.009 452 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.25 % Allowed : 15.21 % Favored : 84.54 % Rotamer: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.35 (0.38), residues: 401 helix: -3.07 (0.85), residues: 27 sheet: -1.40 (0.56), residues: 85 loop : -2.60 (0.33), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 97 TYR 0.027 0.002 TYR A 423 PHE 0.031 0.002 PHE A 486 TRP 0.019 0.002 TRP B 34 HIS 0.007 0.002 HIS C 91 Details of bonding type rmsd covalent geometry : bond 0.00431 ( 3301) covalent geometry : angle 0.71724 ( 4492) SS BOND : bond 0.00505 ( 4) SS BOND : angle 1.97910 ( 8) hydrogen bonds : bond 0.03575 ( 45) hydrogen bonds : angle 8.20108 ( 105) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 802 Ramachandran restraints generated. 401 Oldfield, 0 Emsley, 401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 802 Ramachandran restraints generated. 401 Oldfield, 0 Emsley, 401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 0.071 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 353 TRP cc_start: 0.7212 (p-90) cc_final: 0.6918 (p90) REVERT: A 395 VAL cc_start: 0.6805 (t) cc_final: 0.6564 (t) REVERT: A 465 GLU cc_start: 0.6167 (tt0) cc_final: 0.5862 (tt0) REVERT: A 491 PRO cc_start: 0.7508 (Cg_endo) cc_final: 0.7257 (Cg_exo) REVERT: B 45 LEU cc_start: 0.7670 (mt) cc_final: 0.7324 (mm) outliers start: 0 outliers final: 0 residues processed: 68 average time/residue: 0.0682 time to fit residues: 5.6471 Evaluate side-chains 67 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 1 optimal weight: 0.9980 chunk 39 optimal weight: 0.0970 chunk 30 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 23 optimal weight: 0.5980 chunk 4 optimal weight: 0.3980 chunk 8 optimal weight: 0.9980 chunk 16 optimal weight: 0.4980 chunk 25 optimal weight: 0.9980 chunk 32 optimal weight: 0.0020 chunk 18 optimal weight: 0.9990 overall best weight: 0.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.183971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.168299 restraints weight = 6998.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.171655 restraints weight = 4800.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.174046 restraints weight = 3465.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.175822 restraints weight = 2616.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.177112 restraints weight = 2042.142| |-----------------------------------------------------------------------------| r_work (final): 0.4170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5087 moved from start: 0.7108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 3305 Z= 0.175 Angle : 0.714 5.974 4500 Z= 0.376 Chirality : 0.048 0.234 476 Planarity : 0.006 0.084 578 Dihedral : 6.145 23.911 452 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 12.58 Ramachandran Plot: Outliers : 0.25 % Allowed : 13.97 % Favored : 85.79 % Rotamer: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.50 (0.38), residues: 401 helix: -3.08 (0.85), residues: 27 sheet: -1.54 (0.54), residues: 91 loop : -2.71 (0.33), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 97 TYR 0.009 0.001 TYR A 369 PHE 0.027 0.002 PHE A 486 TRP 0.015 0.002 TRP B 34 HIS 0.009 0.002 HIS C 91 Details of bonding type rmsd covalent geometry : bond 0.00392 ( 3301) covalent geometry : angle 0.71044 ( 4492) SS BOND : bond 0.00435 ( 4) SS BOND : angle 1.84475 ( 8) hydrogen bonds : bond 0.03206 ( 45) hydrogen bonds : angle 8.03198 ( 105) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 802 Ramachandran restraints generated. 401 Oldfield, 0 Emsley, 401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 802 Ramachandran restraints generated. 401 Oldfield, 0 Emsley, 401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 0.075 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 353 TRP cc_start: 0.7206 (p-90) cc_final: 0.5940 (p-90) REVERT: A 491 PRO cc_start: 0.7491 (Cg_endo) cc_final: 0.7252 (Cg_exo) REVERT: B 45 LEU cc_start: 0.7749 (mt) cc_final: 0.7357 (mm) outliers start: 0 outliers final: 0 residues processed: 63 average time/residue: 0.0703 time to fit residues: 5.3149 Evaluate side-chains 62 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 39 optimal weight: 0.9980 chunk 14 optimal weight: 0.1980 chunk 5 optimal weight: 0.4980 chunk 11 optimal weight: 0.6980 chunk 17 optimal weight: 0.7980 chunk 4 optimal weight: 0.0970 chunk 36 optimal weight: 0.0970 chunk 7 optimal weight: 0.5980 chunk 18 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 chunk 8 optimal weight: 0.1980 overall best weight: 0.2176 ------------------------------------------------------------------------------- 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 = 0.4269 r_free = 0.4269 target = 0.184868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.169795 restraints weight = 6827.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.172828 restraints weight = 4697.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.175138 restraints weight = 3428.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.176837 restraints weight = 2598.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.178174 restraints weight = 2041.225| |-----------------------------------------------------------------------------| r_work (final): 0.4183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5067 moved from start: 0.7178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 3305 Z= 0.139 Angle : 0.675 6.013 4500 Z= 0.351 Chirality : 0.046 0.210 476 Planarity : 0.006 0.082 578 Dihedral : 5.703 21.799 452 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.25 % Allowed : 13.22 % Favored : 86.53 % Rotamer: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.39 (0.39), residues: 401 helix: -2.81 (0.87), residues: 27 sheet: -1.58 (0.52), residues: 92 loop : -2.61 (0.35), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 45 TYR 0.024 0.001 TYR A 423 PHE 0.024 0.002 PHE A 486 TRP 0.012 0.002 TRP A 353 HIS 0.007 0.002 HIS C 91 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 3301) covalent geometry : angle 0.67224 ( 4492) SS BOND : bond 0.00458 ( 4) SS BOND : angle 1.65244 ( 8) hydrogen bonds : bond 0.02864 ( 45) hydrogen bonds : angle 7.76468 ( 105) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 802 Ramachandran restraints generated. 401 Oldfield, 0 Emsley, 401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 802 Ramachandran restraints generated. 401 Oldfield, 0 Emsley, 401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 0.117 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 353 TRP cc_start: 0.7224 (p-90) cc_final: 0.5956 (p-90) REVERT: A 491 PRO cc_start: 0.7479 (Cg_endo) cc_final: 0.7219 (Cg_exo) REVERT: B 45 LEU cc_start: 0.7724 (mt) cc_final: 0.7380 (mm) REVERT: C 42 GLN cc_start: 0.6582 (pp30) cc_final: 0.6294 (pp30) outliers start: 0 outliers final: 0 residues processed: 65 average time/residue: 0.0798 time to fit residues: 6.2182 Evaluate side-chains 64 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 18 optimal weight: 0.9980 chunk 33 optimal weight: 0.5980 chunk 7 optimal weight: 0.0970 chunk 9 optimal weight: 0.5980 chunk 30 optimal weight: 0.1980 chunk 2 optimal weight: 0.0470 chunk 12 optimal weight: 0.5980 chunk 6 optimal weight: 0.0060 chunk 29 optimal weight: 0.7980 chunk 35 optimal weight: 0.0170 chunk 1 optimal weight: 0.5980 overall best weight: 0.0730 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 505 HIS ** C 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.186571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.173022 restraints weight = 7148.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.175956 restraints weight = 4933.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.178129 restraints weight = 3561.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.179785 restraints weight = 2660.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.181005 restraints weight = 2042.035| |-----------------------------------------------------------------------------| r_work (final): 0.4216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4981 moved from start: 0.7115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 3305 Z= 0.104 Angle : 0.613 5.916 4500 Z= 0.313 Chirality : 0.045 0.208 476 Planarity : 0.006 0.081 578 Dihedral : 4.876 21.338 452 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.25 % Allowed : 11.72 % Favored : 88.03 % Rotamer: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.14 (0.39), residues: 401 helix: -2.78 (0.83), residues: 27 sheet: -1.20 (0.51), residues: 94 loop : -2.51 (0.36), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 45 TYR 0.011 0.001 TYR A 369 PHE 0.010 0.001 PHE C 83 TRP 0.011 0.001 TRP A 353 HIS 0.007 0.003 HIS A 505 Details of bonding type rmsd covalent geometry : bond 0.00250 ( 3301) covalent geometry : angle 0.61013 ( 4492) SS BOND : bond 0.00308 ( 4) SS BOND : angle 1.43870 ( 8) hydrogen bonds : bond 0.02425 ( 45) hydrogen bonds : angle 7.34835 ( 105) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 966.60 seconds wall clock time: 17 minutes 15.34 seconds (1035.34 seconds total)