Starting phenix.real_space_refine on Fri Sep 11 01:53:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6nf6_9361/09_2026/6nf6_9361.cif Found real_map, /net/cci-nas-00/data/ceres_data/6nf6_9361/09_2026/6nf6_9361.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.32 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6nf6_9361/09_2026/6nf6_9361.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6nf6_9361/09_2026/6nf6_9361.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6nf6_9361/09_2026/6nf6_9361.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6nf6_9361/09_2026/6nf6_9361.cif" model { file = "/net/cci-nas-00/data/ceres_data/6nf6_9361/09_2026/6nf6_9361.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6nf6_9361/09_2026/6nf6_9361.cif" } resolution = 3.32 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= 1.000 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 48 5.16 5 C 4428 2.51 5 N 1024 2.21 5 O 1098 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6598 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 411, 3264 Classifications: {'peptide': 411} Link IDs: {'PTRANS': 12, 'TRANS': 398} Chain breaks: 5 Chain: "B" Number of atoms: 3264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 411, 3264 Classifications: {'peptide': 411} Link IDs: {'PTRANS': 12, 'TRANS': 398} Chain breaks: 5 Chain: "A" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'Y01': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'Y01': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.56, per 1000 atoms: 0.24 Number of scatterers: 6598 At special positions: 0 Unit cell: (91.67, 75.19, 75.19, 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 48 16.00 O 1098 8.00 N 1024 7.00 C 4428 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.51 Conformation dependent library (CDL) restraints added in 340.8 milliseconds 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1548 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 0 sheets defined 83.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.10 Creating SS restraints... Processing helix chain 'A' and resid 49 through 78 removed outlier: 3.964A pdb=" N GLY A 53 " --> pdb=" O ALA A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 109 Processing helix chain 'A' and resid 127 through 152 Processing helix chain 'A' and resid 162 through 182 removed outlier: 3.724A pdb=" N HIS A 181 " --> pdb=" O PHE A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 215 Processing helix chain 'A' and resid 216 through 226 removed outlier: 3.820A pdb=" N GLU A 223 " --> pdb=" O HIS A 219 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLN A 225 " --> pdb=" O GLU A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 280 Proline residue: A 261 - end of helix removed outlier: 3.824A pdb=" N THR A 264 " --> pdb=" O TYR A 260 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU A 268 " --> pdb=" O THR A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 328 Processing helix chain 'A' and resid 334 through 365 removed outlier: 3.812A pdb=" N VAL A 338 " --> pdb=" O TYR A 334 " (cutoff:3.500A) Proline residue: A 349 - end of helix Processing helix chain 'A' and resid 376 through 405 removed outlier: 4.212A pdb=" N GLY A 390 " --> pdb=" O GLY A 386 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N GLN A 391 " --> pdb=" O ALA A 387 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N THR A 405 " --> pdb=" O ALA A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 437 removed outlier: 3.589A pdb=" N LEU A 416 " --> pdb=" O ASN A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 509 Processing helix chain 'A' and resid 510 through 512 No H-bonds generated for 'chain 'A' and resid 510 through 512' Processing helix chain 'A' and resid 528 through 559 Proline residue: A 541 - end of helix removed outlier: 3.525A pdb=" N VAL A 559 " --> pdb=" O LEU A 555 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 78 Processing helix chain 'B' and resid 83 through 109 Processing helix chain 'B' and resid 127 through 152 Processing helix chain 'B' and resid 162 through 182 removed outlier: 3.724A pdb=" N HIS B 181 " --> pdb=" O PHE B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 215 Processing helix chain 'B' and resid 216 through 226 removed outlier: 3.820A pdb=" N GLU B 223 " --> pdb=" O HIS B 219 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLN B 225 " --> pdb=" O GLU B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 280 Proline residue: B 261 - end of helix removed outlier: 3.824A pdb=" N THR B 264 " --> pdb=" O TYR B 260 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU B 268 " --> pdb=" O THR B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 328 Processing helix chain 'B' and resid 334 through 365 removed outlier: 3.812A pdb=" N VAL B 338 " --> pdb=" O TYR B 334 " (cutoff:3.500A) Proline residue: B 349 - end of helix Processing helix chain 'B' and resid 376 through 405 removed outlier: 4.212A pdb=" N GLY B 390 " --> pdb=" O GLY B 386 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N GLN B 391 " --> pdb=" O ALA B 387 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N THR B 405 " --> pdb=" O ALA B 401 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 437 removed outlier: 3.589A pdb=" N LEU B 416 " --> pdb=" O ASN B 412 " (cutoff:3.500A) Processing helix chain 'B' and resid 488 through 509 Processing helix chain 'B' and resid 510 through 512 No H-bonds generated for 'chain 'B' and resid 510 through 512' Processing helix chain 'B' and resid 528 through 559 Proline residue: B 541 - end of helix removed outlier: 3.525A pdb=" N VAL B 559 " --> pdb=" O LEU B 555 " (cutoff:3.500A) 536 hydrogen bonds defined for protein. 1608 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: 0.92 Time building geometry restraints manager: 0.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1136 1.33 - 1.45: 1756 1.45 - 1.57: 3800 1.57 - 1.69: 0 1.69 - 1.81: 72 Bond restraints: 6764 Sorted by residual: bond pdb=" CAX Y01 A 601 " pdb=" OAH Y01 A 601 " ideal model delta sigma weight residual 1.248 1.342 -0.094 2.00e-02 2.50e+03 2.21e+01 bond pdb=" CAX Y01 B 601 " pdb=" OAH Y01 B 601 " ideal model delta sigma weight residual 1.248 1.341 -0.093 2.00e-02 2.50e+03 2.18e+01 bond pdb=" C GLN A 112 " pdb=" N PRO A 113 " ideal model delta sigma weight residual 1.332 1.361 -0.029 1.12e-02 7.97e+03 6.52e+00 bond pdb=" C GLN B 112 " pdb=" N PRO B 113 " ideal model delta sigma weight residual 1.332 1.361 -0.029 1.12e-02 7.97e+03 6.52e+00 bond pdb=" C ASN A 280 " pdb=" N VAL A 281 " ideal model delta sigma weight residual 1.335 1.306 0.029 1.16e-02 7.43e+03 6.31e+00 ... (remaining 6759 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.99: 8779 1.99 - 3.97: 337 3.97 - 5.96: 68 5.96 - 7.95: 20 7.95 - 9.93: 6 Bond angle restraints: 9210 Sorted by residual: angle pdb=" CA GLY B 528 " pdb=" C GLY B 528 " pdb=" O GLY B 528 " ideal model delta sigma weight residual 122.22 119.74 2.48 6.50e-01 2.37e+00 1.46e+01 angle pdb=" CA GLY A 528 " pdb=" C GLY A 528 " pdb=" O GLY A 528 " ideal model delta sigma weight residual 122.22 119.74 2.48 6.50e-01 2.37e+00 1.46e+01 angle pdb=" C MET B 277 " pdb=" N TRP B 278 " pdb=" CA TRP B 278 " ideal model delta sigma weight residual 122.11 116.69 5.42 1.64e+00 3.72e-01 1.09e+01 angle pdb=" C MET A 277 " pdb=" N TRP A 278 " pdb=" CA TRP A 278 " ideal model delta sigma weight residual 122.11 116.69 5.42 1.64e+00 3.72e-01 1.09e+01 angle pdb=" CA TRP A 101 " pdb=" CB TRP A 101 " pdb=" CG TRP A 101 " ideal model delta sigma weight residual 113.60 107.43 6.17 1.90e+00 2.77e-01 1.06e+01 ... (remaining 9205 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.85: 3344 16.85 - 33.70: 426 33.70 - 50.55: 84 50.55 - 67.39: 18 67.39 - 84.24: 10 Dihedral angle restraints: 3882 sinusoidal: 1484 harmonic: 2398 Sorted by residual: dihedral pdb=" CA ALA B 331 " pdb=" C ALA B 331 " pdb=" N PRO B 332 " pdb=" CA PRO B 332 " ideal model delta harmonic sigma weight residual -180.00 -150.60 -29.40 0 5.00e+00 4.00e-02 3.46e+01 dihedral pdb=" CA ALA A 331 " pdb=" C ALA A 331 " pdb=" N PRO A 332 " pdb=" CA PRO A 332 " ideal model delta harmonic sigma weight residual -180.00 -150.60 -29.40 0 5.00e+00 4.00e-02 3.46e+01 dihedral pdb=" CA ASN B 280 " pdb=" C ASN B 280 " pdb=" N VAL B 281 " pdb=" CA VAL B 281 " ideal model delta harmonic sigma weight residual 180.00 155.48 24.52 0 5.00e+00 4.00e-02 2.41e+01 ... (remaining 3879 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 1002 0.093 - 0.185: 98 0.185 - 0.278: 6 0.278 - 0.370: 2 0.370 - 0.463: 2 Chirality restraints: 1110 Sorted by residual: chirality pdb=" CBG Y01 A 601 " pdb=" CAQ Y01 A 601 " pdb=" CBD Y01 A 601 " pdb=" CBI Y01 A 601 " both_signs ideal model delta sigma weight residual False -2.33 -2.80 0.46 2.00e-01 2.50e+01 5.36e+00 chirality pdb=" CBG Y01 B 601 " pdb=" CAQ Y01 B 601 " pdb=" CBD Y01 B 601 " pdb=" CBI Y01 B 601 " both_signs ideal model delta sigma weight residual False -2.33 -2.79 0.46 2.00e-01 2.50e+01 5.35e+00 chirality pdb=" CBH Y01 B 601 " pdb=" CAT Y01 B 601 " pdb=" CAZ Y01 B 601 " pdb=" CBF Y01 B 601 " both_signs ideal model delta sigma weight residual False -2.85 -2.57 -0.29 2.00e-01 2.50e+01 2.05e+00 ... (remaining 1107 not shown) Planarity restraints: 1082 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 305 " -0.044 5.00e-02 4.00e+02 6.68e-02 7.14e+00 pdb=" N PRO A 306 " 0.116 5.00e-02 4.00e+02 pdb=" CA PRO A 306 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 306 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 305 " 0.044 5.00e-02 4.00e+02 6.68e-02 7.14e+00 pdb=" N PRO B 306 " -0.116 5.00e-02 4.00e+02 pdb=" CA PRO B 306 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO B 306 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR B 260 " 0.039 5.00e-02 4.00e+02 5.77e-02 5.33e+00 pdb=" N PRO B 261 " -0.100 5.00e-02 4.00e+02 pdb=" CA PRO B 261 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 261 " 0.033 5.00e-02 4.00e+02 ... (remaining 1079 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 2049 2.83 - 3.35: 6386 3.35 - 3.86: 11322 3.86 - 4.38: 12375 4.38 - 4.90: 22258 Nonbonded interactions: 54390 Sorted by model distance: nonbonded pdb=" O VAL B 338 " pdb=" OG SER B 342 " model vdw 2.309 3.040 nonbonded pdb=" O VAL A 338 " pdb=" OG SER A 342 " model vdw 2.309 3.040 nonbonded pdb=" O VAL B 65 " pdb=" OG SER B 69 " model vdw 2.315 3.040 nonbonded pdb=" O VAL A 65 " pdb=" OG SER A 69 " model vdw 2.315 3.040 nonbonded pdb=" O GLN A 190 " pdb=" OG1 THR A 194 " model vdw 2.328 3.040 ... (remaining 54385 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' } 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: 0.490 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: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 6.910 Find NCS groups from input model: 0.050 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:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 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 : 0.007 0.094 6764 Z= 0.303 Angle : 0.976 9.934 9210 Z= 0.513 Chirality : 0.060 0.463 1110 Planarity : 0.008 0.067 1082 Dihedral : 15.653 84.243 2334 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.51 % Favored : 95.24 % Rotamer: Outliers : 0.00 % Allowed : 8.84 % Favored : 91.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -2.74 (0.24), residues: 798 helix: -1.19 (0.15), residues: 660 sheet: None (None), residues: 0 loop : -4.17 (0.48), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG B 377 TYR 0.016 0.002 TYR A 275 PHE 0.016 0.002 PHE A 71 TRP 0.030 0.003 TRP A 101 HIS 0.008 0.001 HIS A 549 Details of bonding type rmsd/Z covalent geometry : bond 0.00695 / 0.30 ( 6764) covalent geometry : angle 0.97642 / 0.51 ( 9210) hydrogen bonds : bond 0.10775 / 7.42 ( 536) hydrogen bonds : angle 6.03087 / 4.37 ( 1608) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 204 time to evaluate : 0.179 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 184 LYS cc_start: 0.6887 (tttt) cc_final: 0.6623 (tmtt) REVERT: A 254 LYS cc_start: 0.6552 (mtpt) cc_final: 0.5822 (mmtm) REVERT: A 260 TYR cc_start: 0.8620 (t80) cc_final: 0.8217 (t80) REVERT: A 335 GLN cc_start: 0.8292 (mp10) cc_final: 0.8081 (mp10) REVERT: A 424 PHE cc_start: 0.7969 (t80) cc_final: 0.7662 (t80) REVERT: B 184 LYS cc_start: 0.6878 (tttt) cc_final: 0.6624 (tmtt) REVERT: B 254 LYS cc_start: 0.6525 (mtpt) cc_final: 0.5792 (mmtm) REVERT: B 260 TYR cc_start: 0.8625 (t80) cc_final: 0.8219 (t80) REVERT: B 335 GLN cc_start: 0.8297 (mp10) cc_final: 0.8083 (mp10) REVERT: B 424 PHE cc_start: 0.7974 (t80) cc_final: 0.7669 (t80) outliers start: 0 outliers final: 0 residues processed: 204 average time/residue: 0.0665 time to fit residues: 19.0374 Evaluate side-chains 162 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 162 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 49 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 9.9990 chunk 51 optimal weight: 10.0000 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 0.8980 chunk 74 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 515 HIS B 515 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.155196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.129086 restraints weight = 8033.481| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 1.73 r_work: 0.3335 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3201 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.1536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6764 Z= 0.135 Angle : 0.578 6.410 9210 Z= 0.306 Chirality : 0.040 0.132 1110 Planarity : 0.005 0.057 1082 Dihedral : 6.134 46.695 894 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 1.38 % Allowed : 12.98 % Favored : 85.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 0.40 (0.29), residues: 798 helix: 1.06 (0.18), residues: 680 sheet: None (None), residues: 0 loop : -4.43 (0.54), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 377 TYR 0.013 0.002 TYR A 340 PHE 0.012 0.001 PHE A 178 TRP 0.021 0.002 TRP B 101 HIS 0.006 0.001 HIS B 549 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.14 ( 6764) covalent geometry : angle 0.57751 / 0.31 ( 9210) hydrogen bonds : bond 0.04277 / 2.89 ( 536) hydrogen bonds : angle 4.32204 / 3.16 ( 1608) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 202 time to evaluate : 0.221 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 254 LYS cc_start: 0.6953 (mtpt) cc_final: 0.6114 (mmtm) REVERT: A 260 TYR cc_start: 0.8629 (t80) cc_final: 0.8407 (t80) REVERT: A 424 PHE cc_start: 0.8227 (t80) cc_final: 0.8008 (t80) REVERT: A 546 TYR cc_start: 0.8316 (t80) cc_final: 0.8057 (t80) REVERT: B 254 LYS cc_start: 0.6940 (mtpt) cc_final: 0.6113 (mmtm) REVERT: B 260 TYR cc_start: 0.8619 (t80) cc_final: 0.8397 (t80) REVERT: B 424 PHE cc_start: 0.8187 (t80) cc_final: 0.7969 (t80) REVERT: B 546 TYR cc_start: 0.8311 (t80) cc_final: 0.8051 (t80) outliers start: 10 outliers final: 6 residues processed: 204 average time/residue: 0.0682 time to fit residues: 19.5191 Evaluate side-chains 184 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 178 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 278 TRP Chi-restraints excluded: chain A residue 487 TRP Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain B residue 278 TRP Chi-restraints excluded: chain B residue 487 TRP Chi-restraints excluded: chain B residue 559 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 53 optimal weight: 0.4980 chunk 58 optimal weight: 9.9990 chunk 9 optimal weight: 0.6980 chunk 12 optimal weight: 0.9980 chunk 80 optimal weight: 0.9990 chunk 18 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 52 optimal weight: 0.6980 chunk 71 optimal weight: 0.0170 chunk 4 optimal weight: 1.9990 overall best weight: 0.5818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 324 GLN B 324 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.156911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.130665 restraints weight = 7881.292| |-----------------------------------------------------------------------------| r_work (start): 0.3501 rms_B_bonded: 1.71 r_work: 0.3358 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3225 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.2032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6764 Z= 0.121 Angle : 0.562 6.408 9210 Z= 0.293 Chirality : 0.040 0.220 1110 Planarity : 0.004 0.053 1082 Dihedral : 5.756 48.442 894 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.01 % Favored : 94.74 % Rotamer: Outliers : 1.93 % Allowed : 15.75 % Favored : 82.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 1.45 (0.30), residues: 798 helix: 1.83 (0.19), residues: 684 sheet: None (None), residues: 0 loop : -4.74 (0.51), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 377 TYR 0.016 0.001 TYR B 340 PHE 0.019 0.001 PHE A 320 TRP 0.016 0.002 TRP A 101 HIS 0.003 0.001 HIS B 549 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 ( 6764) covalent geometry : angle 0.56164 / 0.29 ( 9210) hydrogen bonds : bond 0.03939 / 2.66 ( 536) hydrogen bonds : angle 4.14429 / 3.04 ( 1608) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 188 time to evaluate : 0.237 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 254 LYS cc_start: 0.6842 (mtpt) cc_final: 0.6263 (mmtm) REVERT: A 546 TYR cc_start: 0.8314 (t80) cc_final: 0.8022 (t80) REVERT: B 254 LYS cc_start: 0.6827 (mtpt) cc_final: 0.6237 (mmtm) REVERT: B 546 TYR cc_start: 0.8304 (t80) cc_final: 0.8010 (t80) outliers start: 14 outliers final: 10 residues processed: 190 average time/residue: 0.0658 time to fit residues: 17.5207 Evaluate side-chains 176 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 166 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 278 TRP Chi-restraints excluded: chain A residue 487 TRP Chi-restraints excluded: chain A residue 548 MET Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 278 TRP Chi-restraints excluded: chain B residue 487 TRP Chi-restraints excluded: chain B residue 548 MET Chi-restraints excluded: chain B residue 559 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 17 optimal weight: 10.0000 chunk 25 optimal weight: 0.7980 chunk 48 optimal weight: 0.8980 chunk 3 optimal weight: 0.7980 chunk 74 optimal weight: 0.9980 chunk 58 optimal weight: 8.9990 chunk 11 optimal weight: 1.9990 chunk 54 optimal weight: 10.0000 chunk 14 optimal weight: 2.9990 chunk 71 optimal weight: 6.9990 chunk 81 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.155568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.129247 restraints weight = 8056.344| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 1.76 r_work: 0.3350 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3219 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.2297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6764 Z= 0.134 Angle : 0.573 6.467 9210 Z= 0.304 Chirality : 0.041 0.183 1110 Planarity : 0.004 0.051 1082 Dihedral : 5.658 50.465 894 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.51 % Favored : 94.24 % Rotamer: Outliers : 1.80 % Allowed : 17.82 % Favored : 80.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 1.83 (0.31), residues: 798 helix: 2.10 (0.19), residues: 684 sheet: None (None), residues: 0 loop : -4.72 (0.53), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 377 TYR 0.010 0.001 TYR A 529 PHE 0.010 0.001 PHE A 178 TRP 0.015 0.002 TRP A 101 HIS 0.003 0.001 HIS A 549 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.13 ( 6764) covalent geometry : angle 0.57268 / 0.30 ( 9210) hydrogen bonds : bond 0.03984 / 2.69 ( 536) hydrogen bonds : angle 4.20597 / 3.07 ( 1608) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 184 time to evaluate : 0.276 Fit side-chains REVERT: A 162 ILE cc_start: 0.8745 (mp) cc_final: 0.8311 (pt) REVERT: A 546 TYR cc_start: 0.8298 (t80) cc_final: 0.7991 (t80) REVERT: B 162 ILE cc_start: 0.8788 (mp) cc_final: 0.8336 (pt) REVERT: B 546 TYR cc_start: 0.8295 (t80) cc_final: 0.7984 (t80) outliers start: 13 outliers final: 12 residues processed: 186 average time/residue: 0.0744 time to fit residues: 19.3622 Evaluate side-chains 178 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 166 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 278 TRP Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 487 TRP Chi-restraints excluded: chain A residue 548 MET Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 278 TRP Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 487 TRP Chi-restraints excluded: chain B residue 548 MET Chi-restraints excluded: chain B residue 559 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 47 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 78 optimal weight: 3.9990 chunk 37 optimal weight: 5.9990 chunk 75 optimal weight: 0.5980 chunk 50 optimal weight: 0.0670 chunk 70 optimal weight: 0.8980 chunk 76 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 7 optimal weight: 4.9990 overall best weight: 0.9122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.156188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.129680 restraints weight = 8108.005| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 1.77 r_work: 0.3355 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3225 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.2473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 6764 Z= 0.136 Angle : 0.580 6.532 9210 Z= 0.309 Chirality : 0.040 0.160 1110 Planarity : 0.004 0.050 1082 Dihedral : 5.582 52.312 894 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.26 % Favored : 94.49 % Rotamer: Outliers : 2.07 % Allowed : 17.54 % Favored : 80.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 1.96 (0.31), residues: 798 helix: 2.20 (0.19), residues: 684 sheet: None (None), residues: 0 loop : -4.71 (0.52), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 489 TYR 0.017 0.002 TYR A 340 PHE 0.021 0.001 PHE A 320 TRP 0.016 0.002 TRP A 127 HIS 0.003 0.001 HIS B 549 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 ( 6764) covalent geometry : angle 0.58005 / 0.31 ( 9210) hydrogen bonds : bond 0.04007 / 2.70 ( 536) hydrogen bonds : angle 4.22489 / 3.08 ( 1608) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 180 time to evaluate : 0.259 Fit side-chains REVERT: A 162 ILE cc_start: 0.8704 (mp) cc_final: 0.8286 (pt) REVERT: A 199 MET cc_start: 0.7811 (mmt) cc_final: 0.7285 (mmt) REVERT: A 546 TYR cc_start: 0.8289 (t80) cc_final: 0.7993 (t80) REVERT: B 162 ILE cc_start: 0.8747 (mp) cc_final: 0.8315 (pt) REVERT: B 199 MET cc_start: 0.7782 (mmt) cc_final: 0.7244 (mmt) REVERT: B 546 TYR cc_start: 0.8285 (t80) cc_final: 0.7986 (t80) outliers start: 15 outliers final: 13 residues processed: 183 average time/residue: 0.0715 time to fit residues: 18.5291 Evaluate side-chains 177 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 164 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 278 TRP Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 487 TRP Chi-restraints excluded: chain A residue 548 MET Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 278 TRP Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 487 TRP Chi-restraints excluded: chain B residue 548 MET Chi-restraints excluded: chain B residue 559 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 38 optimal weight: 0.7980 chunk 9 optimal weight: 0.7980 chunk 1 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 73 optimal weight: 0.7980 chunk 63 optimal weight: 0.8980 chunk 46 optimal weight: 2.9990 chunk 71 optimal weight: 0.7980 chunk 13 optimal weight: 4.9990 chunk 60 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.157128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.130600 restraints weight = 8012.970| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 1.76 r_work: 0.3367 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3238 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.2573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6764 Z= 0.131 Angle : 0.589 6.404 9210 Z= 0.314 Chirality : 0.041 0.203 1110 Planarity : 0.004 0.049 1082 Dihedral : 5.518 54.011 894 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.01 % Favored : 94.74 % Rotamer: Outliers : 2.49 % Allowed : 18.23 % Favored : 79.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 2.07 (0.31), residues: 798 helix: 2.27 (0.19), residues: 684 sheet: None (None), residues: 0 loop : -4.66 (0.52), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 377 TYR 0.018 0.001 TYR A 340 PHE 0.009 0.001 PHE B 178 TRP 0.014 0.002 TRP A 487 HIS 0.003 0.001 HIS B 549 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 ( 6764) covalent geometry : angle 0.58902 / 0.31 ( 9210) hydrogen bonds : bond 0.03972 / 2.68 ( 536) hydrogen bonds : angle 4.23000 / 3.08 ( 1608) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 179 time to evaluate : 0.248 Fit side-chains REVERT: A 162 ILE cc_start: 0.8722 (mp) cc_final: 0.8310 (pt) REVERT: A 223 GLU cc_start: 0.8088 (OUTLIER) cc_final: 0.7475 (mp0) REVERT: B 162 ILE cc_start: 0.8761 (mp) cc_final: 0.8334 (pt) REVERT: B 223 GLU cc_start: 0.8105 (OUTLIER) cc_final: 0.7496 (mp0) outliers start: 18 outliers final: 12 residues processed: 183 average time/residue: 0.0774 time to fit residues: 19.5152 Evaluate side-chains 175 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 161 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 223 GLU Chi-restraints excluded: chain A residue 278 TRP Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 548 MET Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 223 GLU Chi-restraints excluded: chain B residue 278 TRP Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 548 MET Chi-restraints excluded: chain B residue 559 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 21 optimal weight: 0.9990 chunk 50 optimal weight: 0.6980 chunk 11 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 60 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 40 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 overall best weight: 0.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.157545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.131409 restraints weight = 7998.200| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 1.75 r_work: 0.3382 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3249 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.2689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 6764 Z= 0.136 Angle : 0.596 6.270 9210 Z= 0.316 Chirality : 0.041 0.168 1110 Planarity : 0.004 0.048 1082 Dihedral : 5.512 55.754 894 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 2.49 % Allowed : 17.96 % Favored : 79.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 2.07 (0.31), residues: 798 helix: 2.27 (0.19), residues: 684 sheet: None (None), residues: 0 loop : -4.66 (0.51), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 547 TYR 0.026 0.002 TYR B 546 PHE 0.017 0.001 PHE A 320 TRP 0.012 0.002 TRP A 127 HIS 0.003 0.001 HIS A 549 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 ( 6764) covalent geometry : angle 0.59557 / 0.32 ( 9210) hydrogen bonds : bond 0.04018 / 2.73 ( 536) hydrogen bonds : angle 4.21876 / 3.07 ( 1608) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 170 time to evaluate : 0.275 Fit side-chains REVERT: A 162 ILE cc_start: 0.8724 (mp) cc_final: 0.8291 (pt) REVERT: A 279 LYS cc_start: 0.7639 (tptt) cc_final: 0.7314 (tttp) REVERT: B 162 ILE cc_start: 0.8764 (mp) cc_final: 0.8317 (pt) REVERT: B 279 LYS cc_start: 0.7627 (tptt) cc_final: 0.7307 (tttp) outliers start: 18 outliers final: 16 residues processed: 178 average time/residue: 0.0674 time to fit residues: 16.9789 Evaluate side-chains 183 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 167 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 278 TRP Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 548 MET Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 278 TRP Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 548 MET Chi-restraints excluded: chain B residue 557 VAL Chi-restraints excluded: chain B residue 559 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 9 optimal weight: 0.8980 chunk 76 optimal weight: 4.9990 chunk 38 optimal weight: 0.9990 chunk 19 optimal weight: 0.9990 chunk 69 optimal weight: 0.6980 chunk 81 optimal weight: 0.7980 chunk 55 optimal weight: 3.9990 chunk 56 optimal weight: 0.9990 chunk 23 optimal weight: 3.9990 chunk 53 optimal weight: 0.0870 chunk 21 optimal weight: 3.9990 overall best weight: 0.6960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.160062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.134142 restraints weight = 8023.258| |-----------------------------------------------------------------------------| r_work (start): 0.3540 rms_B_bonded: 1.74 r_work: 0.3404 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3273 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.2787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6764 Z= 0.129 Angle : 0.603 7.669 9210 Z= 0.323 Chirality : 0.041 0.178 1110 Planarity : 0.004 0.048 1082 Dihedral : 5.427 56.172 894 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 3.31 % Allowed : 17.13 % Favored : 79.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 2.13 (0.31), residues: 798 helix: 2.31 (0.19), residues: 684 sheet: None (None), residues: 0 loop : -4.69 (0.51), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 129 TYR 0.021 0.002 TYR B 426 PHE 0.008 0.001 PHE B 178 TRP 0.012 0.002 TRP A 101 HIS 0.002 0.000 HIS A 549 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 ( 6764) covalent geometry : angle 0.60321 / 0.32 ( 9210) hydrogen bonds : bond 0.03968 / 2.69 ( 536) hydrogen bonds : angle 4.25711 / 3.08 ( 1608) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 169 time to evaluate : 0.254 Fit side-chains REVERT: A 162 ILE cc_start: 0.8777 (mp) cc_final: 0.8311 (pt) REVERT: A 223 GLU cc_start: 0.8104 (OUTLIER) cc_final: 0.7799 (mp0) REVERT: B 162 ILE cc_start: 0.8796 (mp) cc_final: 0.8328 (pt) REVERT: B 223 GLU cc_start: 0.8097 (OUTLIER) cc_final: 0.7777 (mp0) outliers start: 24 outliers final: 18 residues processed: 181 average time/residue: 0.0648 time to fit residues: 16.6246 Evaluate side-chains 185 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 165 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 223 GLU Chi-restraints excluded: chain A residue 278 TRP Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 548 MET Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 110 SER Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 223 GLU Chi-restraints excluded: chain B residue 278 TRP Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 548 MET Chi-restraints excluded: chain B residue 557 VAL Chi-restraints excluded: chain B residue 559 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 5 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 33 optimal weight: 0.6980 chunk 78 optimal weight: 6.9990 chunk 39 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 68 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 47 optimal weight: 0.0040 chunk 40 optimal weight: 0.9990 overall best weight: 0.6992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.160591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.134427 restraints weight = 8042.962| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 1.77 r_work: 0.3408 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3275 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.2893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6764 Z= 0.132 Angle : 0.624 9.882 9210 Z= 0.331 Chirality : 0.041 0.201 1110 Planarity : 0.004 0.048 1082 Dihedral : 5.405 56.342 894 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 2.76 % Allowed : 19.20 % Favored : 78.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 2.23 (0.31), residues: 798 helix: 2.37 (0.19), residues: 684 sheet: None (None), residues: 0 loop : -4.53 (0.51), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 129 TYR 0.026 0.002 TYR B 426 PHE 0.021 0.001 PHE A 320 TRP 0.012 0.002 TRP B 101 HIS 0.002 0.000 HIS A 549 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 ( 6764) covalent geometry : angle 0.62412 / 0.33 ( 9210) hydrogen bonds : bond 0.03930 / 2.66 ( 536) hydrogen bonds : angle 4.25149 / 3.08 ( 1608) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 167 time to evaluate : 0.219 Fit side-chains REVERT: A 162 ILE cc_start: 0.8798 (mp) cc_final: 0.8370 (pt) REVERT: A 223 GLU cc_start: 0.8065 (OUTLIER) cc_final: 0.7429 (mp0) REVERT: B 162 ILE cc_start: 0.8828 (mp) cc_final: 0.8372 (pt) REVERT: B 223 GLU cc_start: 0.8061 (OUTLIER) cc_final: 0.7453 (mp0) outliers start: 20 outliers final: 18 residues processed: 175 average time/residue: 0.0675 time to fit residues: 16.8968 Evaluate side-chains 183 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 163 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 223 GLU Chi-restraints excluded: chain A residue 278 TRP Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 548 MET Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 110 SER Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 223 GLU Chi-restraints excluded: chain B residue 278 TRP Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 548 MET Chi-restraints excluded: chain B residue 557 VAL Chi-restraints excluded: chain B residue 559 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 10 optimal weight: 0.0070 chunk 65 optimal weight: 0.7980 chunk 20 optimal weight: 3.9990 chunk 63 optimal weight: 6.9990 chunk 58 optimal weight: 10.0000 chunk 42 optimal weight: 0.6980 chunk 5 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 43 optimal weight: 0.6980 chunk 48 optimal weight: 2.9990 overall best weight: 1.0400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.159099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.133234 restraints weight = 7945.538| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 1.72 r_work: 0.3402 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3272 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.2921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 6764 Z= 0.145 Angle : 0.634 9.694 9210 Z= 0.339 Chirality : 0.042 0.188 1110 Planarity : 0.004 0.048 1082 Dihedral : 5.509 57.031 894 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.26 % Favored : 95.49 % Rotamer: Outliers : 2.76 % Allowed : 19.20 % Favored : 78.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 2.11 (0.31), residues: 798 helix: 2.32 (0.19), residues: 680 sheet: None (None), residues: 0 loop : -4.56 (0.51), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 129 TYR 0.026 0.002 TYR B 426 PHE 0.010 0.001 PHE B 178 TRP 0.013 0.002 TRP A 180 HIS 0.002 0.001 HIS A 549 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.15 ( 6764) covalent geometry : angle 0.63436 / 0.34 ( 9210) hydrogen bonds : bond 0.04023 / 2.73 ( 536) hydrogen bonds : angle 4.28052 / 3.12 ( 1608) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 159 time to evaluate : 0.191 Fit side-chains REVERT: A 162 ILE cc_start: 0.8813 (mp) cc_final: 0.8331 (pt) REVERT: A 223 GLU cc_start: 0.8015 (OUTLIER) cc_final: 0.7420 (mp0) REVERT: B 162 ILE cc_start: 0.8842 (mp) cc_final: 0.8347 (pt) REVERT: B 223 GLU cc_start: 0.8026 (OUTLIER) cc_final: 0.7397 (mp0) outliers start: 20 outliers final: 18 residues processed: 167 average time/residue: 0.0696 time to fit residues: 16.4564 Evaluate side-chains 176 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 156 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 223 GLU Chi-restraints excluded: chain A residue 278 TRP Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 548 MET Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 110 SER Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 223 GLU Chi-restraints excluded: chain B residue 278 TRP Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 548 MET Chi-restraints excluded: chain B residue 557 VAL Chi-restraints excluded: chain B residue 559 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 16 optimal weight: 6.9990 chunk 74 optimal weight: 0.9980 chunk 22 optimal weight: 0.7980 chunk 49 optimal weight: 2.9990 chunk 60 optimal weight: 0.6980 chunk 23 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 54 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 57 optimal weight: 5.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 114 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.159690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.133474 restraints weight = 7978.292| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 1.74 r_work: 0.3397 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3267 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.2928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 6764 Z= 0.149 Angle : 0.642 9.763 9210 Z= 0.343 Chirality : 0.042 0.185 1110 Planarity : 0.004 0.047 1082 Dihedral : 5.525 57.208 894 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 3.04 % Allowed : 19.48 % Favored : 77.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 2.13 (0.31), residues: 798 helix: 2.34 (0.19), residues: 678 sheet: None (None), residues: 0 loop : -4.47 (0.51), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 129 TYR 0.026 0.002 TYR B 426 PHE 0.021 0.001 PHE A 320 TRP 0.029 0.002 TRP B 180 HIS 0.002 0.001 HIS A 549 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.15 ( 6764) covalent geometry : angle 0.64198 / 0.34 ( 9210) hydrogen bonds : bond 0.04076 / 2.76 ( 536) hydrogen bonds : angle 4.32566 / 3.14 ( 1608) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1741.86 seconds wall clock time: 30 minutes 41.11 seconds (1841.11 seconds total)