Starting phenix.real_space_refine on Wed Jul 1 23:40:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9krh_62527/07_2026/9krh_62527_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9krh_62527/07_2026/9krh_62527.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9krh_62527/07_2026/9krh_62527.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9krh_62527/07_2026/9krh_62527.map" model { file = "/net/cci-nas-00/data/ceres_data/9krh_62527/07_2026/9krh_62527_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9krh_62527/07_2026/9krh_62527_neut.cif" } resolution = 3.4 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= 0.031 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: 6 Type Number sf(0) Gaussians S 36 5.16 5 Cl 1 4.86 5 Na 1 4.78 5 C 2842 2.51 5 N 653 2.21 5 O 698 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 4231 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 532, 4220 Classifications: {'peptide': 532} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 24, 'TRANS': 507} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "A" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 9 Ad-hoc single atom residues: {' CL': 1, ' NA': 1} Unusual residues: {'CRN': 1} Classifications: {'undetermined': 1} Chain breaks: 2 Time building chain proxies: 0.77, per 1000 atoms: 0.18 Number of scatterers: 4231 At special positions: 0 Unit cell: (82.29, 68.575, 88.62, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 1 17.00 S 36 16.00 Na 1 11.00 O 698 8.00 N 653 7.00 C 2842 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 172 " - pdb=" SG CYS A 181 " 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: 0.22 Conformation dependent library (CDL) restraints added in 93.2 milliseconds 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 968 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 1 sheets defined 81.0% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.12 Creating SS restraints... Processing helix chain 'A' and resid 58 through 68 removed outlier: 3.649A pdb=" N ILE A 62 " --> pdb=" O GLN A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 76 Processing helix chain 'A' and resid 76 through 86 removed outlier: 3.911A pdb=" N TYR A 80 " --> pdb=" O TRP A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 101 Processing helix chain 'A' and resid 101 through 117 Processing helix chain 'A' and resid 121 through 130 removed outlier: 4.019A pdb=" N ILE A 126 " --> pdb=" O VAL A 123 " (cutoff:3.500A) Proline residue: A 128 - end of helix Processing helix chain 'A' and resid 131 through 163 removed outlier: 3.769A pdb=" N TYR A 135 " --> pdb=" O LYS A 131 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ILE A 149 " --> pdb=" O ASN A 145 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N MET A 150 " --> pdb=" O THR A 146 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU A 152 " --> pdb=" O TYR A 148 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N PHE A 163 " --> pdb=" O LEU A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 217 Processing helix chain 'A' and resid 232 through 253 Processing helix chain 'A' and resid 258 through 281 removed outlier: 3.906A pdb=" N TYR A 262 " --> pdb=" O GLY A 258 " (cutoff:3.500A) Proline residue: A 268 - end of helix Processing helix chain 'A' and resid 284 through 294 Processing helix chain 'A' and resid 296 through 301 removed outlier: 3.524A pdb=" N LEU A 300 " --> pdb=" O TRP A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 317 removed outlier: 4.377A pdb=" N TRP A 306 " --> pdb=" O SER A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 331 Processing helix chain 'A' and resid 336 through 371 Processing helix chain 'A' and resid 373 through 377 removed outlier: 3.675A pdb=" N VAL A 377 " --> pdb=" O ILE A 374 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 383 No H-bonds generated for 'chain 'A' and resid 381 through 383' Processing helix chain 'A' and resid 384 through 396 removed outlier: 3.588A pdb=" N TYR A 389 " --> pdb=" O ALA A 385 " (cutoff:3.500A) Proline residue: A 390 - end of helix Processing helix chain 'A' and resid 398 through 433 Processing helix chain 'A' and resid 434 through 438 Processing helix chain 'A' and resid 441 through 463 removed outlier: 4.188A pdb=" N SER A 460 " --> pdb=" O VAL A 456 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N MET A 461 " --> pdb=" O ILE A 457 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N THR A 463 " --> pdb=" O LEU A 459 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 476 removed outlier: 3.724A pdb=" N VAL A 469 " --> pdb=" O GLY A 465 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N TYR A 476 " --> pdb=" O LEU A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 496 removed outlier: 3.604A pdb=" N LEU A 484 " --> pdb=" O GLY A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 512 Processing helix chain 'A' and resid 516 through 526 removed outlier: 4.330A pdb=" N LYS A 520 " --> pdb=" O CYS A 516 " (cutoff:3.500A) Processing helix chain 'A' and resid 526 through 541 Processing helix chain 'A' and resid 554 through 570 Processing helix chain 'A' and resid 570 through 583 Processing helix chain 'A' and resid 586 through 595 Processing sheet with id=AA1, first strand: chain 'A' and resid 546 through 547 293 hydrogen bonds defined for protein. 852 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: 0.72 Time building geometry restraints manager: 0.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1231 1.34 - 1.46: 1211 1.46 - 1.58: 1880 1.58 - 1.70: 0 1.70 - 1.81: 52 Bond restraints: 4374 Sorted by residual: bond pdb=" C2 CRN A 701 " pdb=" N3 CRN A 701 " ideal model delta sigma weight residual 1.374 1.245 0.129 2.00e-02 2.50e+03 4.16e+01 bond pdb=" C2 CRN A 701 " pdb=" N1 CRN A 701 " ideal model delta sigma weight residual 1.371 1.445 -0.074 2.00e-02 2.50e+03 1.35e+01 bond pdb=" N VAL A 70 " pdb=" CA VAL A 70 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.19e-02 7.06e+03 9.31e+00 bond pdb=" N PHE A 68 " pdb=" CA PHE A 68 " ideal model delta sigma weight residual 1.457 1.488 -0.031 1.06e-02 8.90e+03 8.49e+00 bond pdb=" N ILE A 62 " pdb=" CA ILE A 62 " ideal model delta sigma weight residual 1.460 1.495 -0.035 1.21e-02 6.83e+03 8.37e+00 ... (remaining 4369 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.94: 5812 1.94 - 3.88: 137 3.88 - 5.82: 18 5.82 - 7.76: 7 7.76 - 9.70: 2 Bond angle restraints: 5976 Sorted by residual: angle pdb=" C PHE A 68 " pdb=" CA PHE A 68 " pdb=" CB PHE A 68 " ideal model delta sigma weight residual 110.35 119.96 -9.61 1.78e+00 3.16e-01 2.92e+01 angle pdb=" N PHE A 68 " pdb=" CA PHE A 68 " pdb=" CB PHE A 68 " ideal model delta sigma weight residual 111.43 101.73 9.70 1.88e+00 2.83e-01 2.66e+01 angle pdb=" CA PHE A 68 " pdb=" CB PHE A 68 " pdb=" CG PHE A 68 " ideal model delta sigma weight residual 113.80 118.13 -4.33 1.00e+00 1.00e+00 1.88e+01 angle pdb=" C ARG A 77 " pdb=" N PHE A 78 " pdb=" CA PHE A 78 " ideal model delta sigma weight residual 120.58 124.81 -4.23 1.32e+00 5.74e-01 1.03e+01 angle pdb=" CA ASP A 60 " pdb=" CB ASP A 60 " pdb=" CG ASP A 60 " ideal model delta sigma weight residual 112.60 115.60 -3.00 1.00e+00 1.00e+00 8.97e+00 ... (remaining 5971 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.49: 2212 17.49 - 34.98: 170 34.98 - 52.47: 40 52.47 - 69.96: 6 69.96 - 87.45: 1 Dihedral angle restraints: 2429 sinusoidal: 901 harmonic: 1528 Sorted by residual: dihedral pdb=" CB GLU A 543 " pdb=" CG GLU A 543 " pdb=" CD GLU A 543 " pdb=" OE1 GLU A 543 " ideal model delta sinusoidal sigma weight residual 0.00 -87.45 87.45 1 3.00e+01 1.11e-03 1.02e+01 dihedral pdb=" CG ARG A 207 " pdb=" CD ARG A 207 " pdb=" NE ARG A 207 " pdb=" CZ ARG A 207 " ideal model delta sinusoidal sigma weight residual -90.00 -131.84 41.84 2 1.50e+01 4.44e-03 9.49e+00 dihedral pdb=" CB MET A 560 " pdb=" CG MET A 560 " pdb=" SD MET A 560 " pdb=" CE MET A 560 " ideal model delta sinusoidal sigma weight residual -180.00 -122.35 -57.65 3 1.50e+01 4.44e-03 9.45e+00 ... (remaining 2426 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 470 0.044 - 0.088: 148 0.088 - 0.132: 28 0.132 - 0.176: 5 0.176 - 0.220: 2 Chirality restraints: 653 Sorted by residual: chirality pdb=" CA VAL A 66 " pdb=" N VAL A 66 " pdb=" C VAL A 66 " pdb=" CB VAL A 66 " both_signs ideal model delta sigma weight residual False 2.44 2.66 -0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" CA ILE A 62 " pdb=" N ILE A 62 " pdb=" C ILE A 62 " pdb=" CB ILE A 62 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.18 2.00e-01 2.50e+01 8.42e-01 chirality pdb=" CA VAL A 70 " pdb=" N VAL A 70 " pdb=" C VAL A 70 " pdb=" CB VAL A 70 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.15 2.00e-01 2.50e+01 5.94e-01 ... (remaining 650 not shown) Planarity restraints: 727 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 68 " -0.002 2.00e-02 2.50e+03 1.42e-02 3.55e+00 pdb=" CG PHE A 68 " -0.008 2.00e-02 2.50e+03 pdb=" CD1 PHE A 68 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE A 68 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE A 68 " 0.010 2.00e-02 2.50e+03 pdb=" CE2 PHE A 68 " 0.022 2.00e-02 2.50e+03 pdb=" CZ PHE A 68 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 277 " 0.009 2.00e-02 2.50e+03 1.73e-02 3.01e+00 pdb=" C VAL A 277 " -0.030 2.00e-02 2.50e+03 pdb=" O VAL A 277 " 0.011 2.00e-02 2.50e+03 pdb=" N ARG A 278 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 139 " -0.009 2.00e-02 2.50e+03 1.72e-02 2.95e+00 pdb=" C VAL A 139 " 0.030 2.00e-02 2.50e+03 pdb=" O VAL A 139 " -0.011 2.00e-02 2.50e+03 pdb=" N ILE A 140 " -0.010 2.00e-02 2.50e+03 ... (remaining 724 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 631 2.75 - 3.29: 4642 3.29 - 3.83: 7380 3.83 - 4.36: 8628 4.36 - 4.90: 14652 Nonbonded interactions: 35933 Sorted by model distance: nonbonded pdb=" O PHE A 473 " pdb=" OG SER A 477 " model vdw 2.213 3.040 nonbonded pdb=" O GLY A 134 " pdb=" OG SER A 137 " model vdw 2.225 3.040 nonbonded pdb=" O PHE A 315 " pdb=" N6 CRN A 701 " model vdw 2.226 3.120 nonbonded pdb=" OG SER A 316 " pdb="NA NA A 703 " model vdw 2.273 3.210 nonbonded pdb=" O GLN A 442 " pdb=" OG SER A 446 " model vdw 2.286 3.040 ... (remaining 35928 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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 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: 0.990 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: 0.000 Extract box with map and model: 0.050 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.870 Find NCS groups from input model: 0.010 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:1.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 6.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 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 : 0.005 0.129 4375 Z= 0.275 Angle : 0.724 9.700 5978 Z= 0.407 Chirality : 0.045 0.220 653 Planarity : 0.005 0.035 727 Dihedral : 13.225 87.446 1458 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 14.04 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.55 % Favored : 95.27 % Rotamer: Outliers : 0.23 % Allowed : 0.45 % Favored : 99.32 % Cbeta Deviations : 0.21 % 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: 0.13 (0.37), residues: 528 helix: 0.53 (0.26), residues: 370 sheet: None (None), residues: 0 loop : -0.77 (0.53), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 77 TYR 0.020 0.001 TYR A 80 PHE 0.026 0.002 PHE A 68 TRP 0.015 0.002 TRP A 591 HIS 0.004 0.001 HIS A 575 Details of bonding type rmsd/Z covalent geometry : bond 0.00521 / 0.27 ( 4374) covalent geometry : angle 0.72379 / 0.41 ( 5976) SS BOND : bond 0.00168 / 0.09 ( 1) SS BOND : angle 1.17877 / 0.64 ( 2) hydrogen bonds : bond 0.16201 / 11.17 ( 293) hydrogen bonds : angle 7.11313 / 5.12 ( 852) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 176 time to evaluate : 0.145 Fit side-chains revert: symmetry clash REVERT: A 131 LYS cc_start: 0.8337 (ttpp) cc_final: 0.7967 (tttm) REVERT: A 245 LEU cc_start: 0.8851 (tt) cc_final: 0.8549 (tt) REVERT: A 305 VAL cc_start: 0.9319 (m) cc_final: 0.9104 (t) REVERT: A 461 MET cc_start: 0.9047 (mtm) cc_final: 0.8813 (mtp) REVERT: A 535 PHE cc_start: 0.7819 (t80) cc_final: 0.7604 (t80) REVERT: A 560 MET cc_start: 0.7644 (tpt) cc_final: 0.6887 (ttt) REVERT: A 587 MET cc_start: 0.6077 (ptt) cc_final: 0.5274 (mtt) outliers start: 1 outliers final: 1 residues processed: 177 average time/residue: 0.0728 time to fit residues: 16.2148 Evaluate side-chains 103 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 102 time to evaluate : 0.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 24 optimal weight: 0.5980 chunk 48 optimal weight: 0.5980 chunk 26 optimal weight: 2.9990 chunk 2 optimal weight: 0.1980 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 0.0770 chunk 31 optimal weight: 0.6980 chunk 25 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 30 optimal weight: 0.9990 overall best weight: 0.4338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 370 GLN A 373 HIS ** A 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 603 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.158066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.132847 restraints weight = 6729.719| |-----------------------------------------------------------------------------| r_work (start): 0.3606 rms_B_bonded: 2.58 r_work: 0.3489 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.3018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 4375 Z= 0.169 Angle : 0.644 8.903 5978 Z= 0.335 Chirality : 0.041 0.161 653 Planarity : 0.004 0.031 727 Dihedral : 4.710 30.600 578 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.50 % Allowed : 10.68 % Favored : 86.82 % 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: 1.00 (0.37), residues: 528 helix: 1.24 (0.26), residues: 381 sheet: None (None), residues: 0 loop : -0.74 (0.55), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 514 TYR 0.013 0.001 TYR A 542 PHE 0.019 0.002 PHE A 406 TRP 0.012 0.001 TRP A 591 HIS 0.003 0.001 HIS A 373 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.17 ( 4374) covalent geometry : angle 0.64443 / 0.33 ( 5976) SS BOND : bond 0.00029 / 0.02 ( 1) SS BOND : angle 0.71307 / 0.39 ( 2) hydrogen bonds : bond 0.05580 / 3.95 ( 293) hydrogen bonds : angle 5.25664 / 3.91 ( 852) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 120 time to evaluate : 0.145 Fit side-chains REVERT: A 245 LEU cc_start: 0.8906 (tt) cc_final: 0.8698 (tt) REVERT: A 430 LEU cc_start: 0.8903 (OUTLIER) cc_final: 0.8370 (pp) REVERT: A 535 PHE cc_start: 0.7994 (t80) cc_final: 0.7688 (t80) REVERT: A 560 MET cc_start: 0.7943 (tpt) cc_final: 0.6952 (ttt) REVERT: A 587 MET cc_start: 0.6000 (ptt) cc_final: 0.5052 (mtt) outliers start: 11 outliers final: 7 residues processed: 123 average time/residue: 0.0489 time to fit residues: 8.2517 Evaluate side-chains 107 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 99 time to evaluate : 0.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 242 CYS Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 430 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 35 optimal weight: 0.5980 chunk 15 optimal weight: 2.9990 chunk 6 optimal weight: 0.7980 chunk 46 optimal weight: 0.9980 chunk 50 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 44 optimal weight: 0.8980 chunk 36 optimal weight: 0.3980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 74 ASN ** A 538 ASN ** 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 = 0.3861 r_free = 0.3861 target = 0.154438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.129547 restraints weight = 6669.164| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 2.54 r_work: 0.3298 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.3524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 4375 Z= 0.175 Angle : 0.605 6.084 5978 Z= 0.318 Chirality : 0.041 0.161 653 Planarity : 0.004 0.033 727 Dihedral : 4.833 39.832 576 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 3.41 % Allowed : 14.32 % Favored : 82.27 % 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: 1.18 (0.37), residues: 528 helix: 1.43 (0.27), residues: 379 sheet: None (None), residues: 0 loop : -0.84 (0.54), residues: 149 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 514 TYR 0.019 0.002 TYR A 542 PHE 0.020 0.002 PHE A 419 TRP 0.013 0.002 TRP A 562 HIS 0.002 0.001 HIS A 603 Details of bonding type rmsd/Z covalent geometry : bond 0.00411 / 0.18 ( 4374) covalent geometry : angle 0.60551 / 0.32 ( 5976) SS BOND : bond 0.00145 / 0.08 ( 1) SS BOND : angle 0.52997 / 0.29 ( 2) hydrogen bonds : bond 0.05134 / 3.59 ( 293) hydrogen bonds : angle 5.01374 / 3.74 ( 852) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 116 time to evaluate : 0.151 Fit side-chains REVERT: A 369 GLU cc_start: 0.7803 (tm-30) cc_final: 0.7443 (tm-30) REVERT: A 430 LEU cc_start: 0.8847 (OUTLIER) cc_final: 0.8335 (pp) REVERT: A 519 MET cc_start: 0.7955 (tpp) cc_final: 0.7438 (mmt) REVERT: A 535 PHE cc_start: 0.7967 (t80) cc_final: 0.7668 (t80) REVERT: A 560 MET cc_start: 0.8063 (tpt) cc_final: 0.7099 (ttt) REVERT: A 587 MET cc_start: 0.6080 (ptt) cc_final: 0.5171 (mtt) outliers start: 15 outliers final: 11 residues processed: 121 average time/residue: 0.0464 time to fit residues: 7.9210 Evaluate side-chains 113 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 101 time to evaluate : 0.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 242 CYS Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 313 ILE Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 529 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 40 optimal weight: 0.9980 chunk 1 optimal weight: 0.7980 chunk 50 optimal weight: 0.1980 chunk 48 optimal weight: 0.6980 chunk 51 optimal weight: 7.9990 chunk 41 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 20 optimal weight: 0.5980 chunk 4 optimal weight: 0.9980 chunk 8 optimal weight: 0.1980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 373 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.155517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.130676 restraints weight = 6691.628| |-----------------------------------------------------------------------------| r_work (start): 0.3571 rms_B_bonded: 2.55 r_work: 0.3455 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.3860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4375 Z= 0.142 Angle : 0.579 7.854 5978 Z= 0.302 Chirality : 0.041 0.169 653 Planarity : 0.004 0.037 727 Dihedral : 4.745 41.672 576 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 3.64 % Allowed : 15.68 % Favored : 80.68 % 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: 1.29 (0.38), residues: 528 helix: 1.58 (0.27), residues: 378 sheet: None (None), residues: 0 loop : -1.00 (0.54), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 514 TYR 0.013 0.001 TYR A 147 PHE 0.026 0.002 PHE A 263 TRP 0.011 0.001 TRP A 124 HIS 0.003 0.001 HIS A 373 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 ( 4374) covalent geometry : angle 0.57893 / 0.30 ( 5976) SS BOND : bond 0.00100 / 0.05 ( 1) SS BOND : angle 0.44899 / 0.24 ( 2) hydrogen bonds : bond 0.04744 / 3.29 ( 293) hydrogen bonds : angle 4.83282 / 3.62 ( 852) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 113 time to evaluate : 0.171 Fit side-chains REVERT: A 94 TYR cc_start: 0.8776 (t80) cc_final: 0.8275 (t80) REVERT: A 369 GLU cc_start: 0.7738 (tm-30) cc_final: 0.7331 (tm-30) REVERT: A 430 LEU cc_start: 0.8822 (OUTLIER) cc_final: 0.8250 (pp) REVERT: A 513 TYR cc_start: 0.7907 (p90) cc_final: 0.7697 (p90) REVERT: A 519 MET cc_start: 0.7817 (tpp) cc_final: 0.7387 (mmt) REVERT: A 535 PHE cc_start: 0.7986 (t80) cc_final: 0.7697 (t80) REVERT: A 560 MET cc_start: 0.8019 (tpt) cc_final: 0.7176 (ttm) REVERT: A 587 MET cc_start: 0.6091 (ptt) cc_final: 0.5125 (mtt) outliers start: 16 outliers final: 11 residues processed: 118 average time/residue: 0.0504 time to fit residues: 8.3868 Evaluate side-chains 113 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 101 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 313 ILE Chi-restraints excluded: chain A residue 329 SER Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 529 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 21 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 29 optimal weight: 0.6980 chunk 17 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 chunk 47 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 49 optimal weight: 0.4980 chunk 46 optimal weight: 0.7980 chunk 5 optimal weight: 0.5980 chunk 35 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 177 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.153633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.128042 restraints weight = 6654.527| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 2.63 r_work: 0.3411 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.4061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 4375 Z= 0.164 Angle : 0.603 10.210 5978 Z= 0.310 Chirality : 0.041 0.143 653 Planarity : 0.004 0.038 727 Dihedral : 4.845 44.042 576 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 4.55 % Allowed : 16.59 % Favored : 78.86 % 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: 1.46 (0.38), residues: 528 helix: 1.62 (0.27), residues: 374 sheet: None (None), residues: 0 loop : -0.59 (0.56), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 514 TYR 0.024 0.001 TYR A 542 PHE 0.025 0.002 PHE A 419 TRP 0.010 0.001 TRP A 485 HIS 0.002 0.001 HIS A 603 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.16 ( 4374) covalent geometry : angle 0.60273 / 0.31 ( 5976) SS BOND : bond 0.00151 / 0.08 ( 1) SS BOND : angle 0.19424 / 0.10 ( 2) hydrogen bonds : bond 0.04781 / 3.30 ( 293) hydrogen bonds : angle 4.74974 / 3.56 ( 852) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 110 time to evaluate : 0.093 Fit side-chains REVERT: A 338 TYR cc_start: 0.8498 (t80) cc_final: 0.8116 (t80) REVERT: A 369 GLU cc_start: 0.7776 (tm-30) cc_final: 0.7369 (tm-30) REVERT: A 430 LEU cc_start: 0.8821 (OUTLIER) cc_final: 0.8209 (pp) REVERT: A 519 MET cc_start: 0.7723 (tpp) cc_final: 0.7131 (mmt) REVERT: A 535 PHE cc_start: 0.7982 (t80) cc_final: 0.7680 (t80) REVERT: A 560 MET cc_start: 0.8070 (tpt) cc_final: 0.7347 (ttm) REVERT: A 587 MET cc_start: 0.5986 (ptt) cc_final: 0.5031 (mtt) outliers start: 20 outliers final: 16 residues processed: 117 average time/residue: 0.0428 time to fit residues: 7.0265 Evaluate side-chains 120 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 103 time to evaluate : 0.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 313 ILE Chi-restraints excluded: chain A residue 329 SER Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain A residue 511 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 44 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 52 optimal weight: 0.5980 chunk 22 optimal weight: 0.9980 chunk 18 optimal weight: 3.9990 chunk 12 optimal weight: 0.0370 chunk 15 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 48 optimal weight: 0.8980 chunk 26 optimal weight: 0.7980 overall best weight: 0.6258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 373 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.153935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.128421 restraints weight = 6718.926| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 2.65 r_work: 0.3420 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.4338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 4375 Z= 0.159 Angle : 0.608 8.947 5978 Z= 0.312 Chirality : 0.041 0.157 653 Planarity : 0.004 0.038 727 Dihedral : 4.803 43.963 576 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 5.68 % Allowed : 17.50 % Favored : 76.82 % 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: 1.48 (0.38), residues: 528 helix: 1.63 (0.27), residues: 374 sheet: None (None), residues: 0 loop : -0.58 (0.56), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 514 TYR 0.018 0.001 TYR A 542 PHE 0.027 0.002 PHE A 419 TRP 0.011 0.001 TRP A 124 HIS 0.004 0.001 HIS A 373 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.16 ( 4374) covalent geometry : angle 0.60822 / 0.31 ( 5976) SS BOND : bond 0.00141 / 0.07 ( 1) SS BOND : angle 0.10161 / 0.05 ( 2) hydrogen bonds : bond 0.04827 / 3.32 ( 293) hydrogen bonds : angle 4.73412 / 3.59 ( 852) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 102 time to evaluate : 0.215 Fit side-chains REVERT: A 338 TYR cc_start: 0.8608 (t80) cc_final: 0.8309 (t80) REVERT: A 369 GLU cc_start: 0.7831 (tm-30) cc_final: 0.7376 (tm-30) REVERT: A 430 LEU cc_start: 0.8745 (OUTLIER) cc_final: 0.8126 (pp) REVERT: A 519 MET cc_start: 0.7783 (tpp) cc_final: 0.7199 (mmt) REVERT: A 535 PHE cc_start: 0.7988 (t80) cc_final: 0.7692 (t80) REVERT: A 560 MET cc_start: 0.8178 (tpt) cc_final: 0.7324 (ttm) REVERT: A 587 MET cc_start: 0.6004 (ptt) cc_final: 0.5040 (mtt) outliers start: 25 outliers final: 19 residues processed: 112 average time/residue: 0.0403 time to fit residues: 6.5207 Evaluate side-chains 119 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 99 time to evaluate : 0.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 TYR Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 120 SER Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 313 ILE Chi-restraints excluded: chain A residue 329 SER Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain A residue 511 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 5 optimal weight: 0.9990 chunk 24 optimal weight: 0.5980 chunk 11 optimal weight: 0.5980 chunk 1 optimal weight: 0.7980 chunk 41 optimal weight: 0.7980 chunk 45 optimal weight: 0.1980 chunk 15 optimal weight: 2.9990 chunk 26 optimal weight: 0.4980 chunk 21 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 49 optimal weight: 0.8980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 = 0.3864 r_free = 0.3864 target = 0.154682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.128770 restraints weight = 6694.393| |-----------------------------------------------------------------------------| r_work (start): 0.3548 rms_B_bonded: 2.66 r_work: 0.3427 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.4471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 4375 Z= 0.154 Angle : 0.625 8.444 5978 Z= 0.318 Chirality : 0.042 0.175 653 Planarity : 0.004 0.038 727 Dihedral : 4.764 42.235 576 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 5.23 % Allowed : 19.09 % Favored : 75.68 % 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: 1.48 (0.38), residues: 528 helix: 1.63 (0.27), residues: 372 sheet: None (None), residues: 0 loop : -0.55 (0.56), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 514 TYR 0.015 0.001 TYR A 542 PHE 0.026 0.002 PHE A 419 TRP 0.012 0.001 TRP A 124 HIS 0.003 0.001 HIS A 603 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.15 ( 4374) covalent geometry : angle 0.62548 / 0.32 ( 5976) SS BOND : bond 0.00144 / 0.08 ( 1) SS BOND : angle 0.10816 / 0.06 ( 2) hydrogen bonds : bond 0.04832 / 3.35 ( 293) hydrogen bonds : angle 4.74164 / 3.65 ( 852) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 99 time to evaluate : 0.152 Fit side-chains REVERT: A 94 TYR cc_start: 0.8846 (t80) cc_final: 0.8266 (t80) REVERT: A 338 TYR cc_start: 0.8680 (t80) cc_final: 0.8321 (t80) REVERT: A 430 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.8047 (pp) REVERT: A 519 MET cc_start: 0.7714 (tpp) cc_final: 0.7280 (mmt) REVERT: A 535 PHE cc_start: 0.8072 (t80) cc_final: 0.7754 (t80) REVERT: A 536 ILE cc_start: 0.9029 (mm) cc_final: 0.8658 (mt) REVERT: A 560 MET cc_start: 0.8220 (tpt) cc_final: 0.7370 (ttm) REVERT: A 587 MET cc_start: 0.6084 (ptt) cc_final: 0.5105 (mtt) outliers start: 23 outliers final: 18 residues processed: 110 average time/residue: 0.0413 time to fit residues: 6.4693 Evaluate side-chains 116 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 97 time to evaluate : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 TYR Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 313 ILE Chi-restraints excluded: chain A residue 329 SER Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 461 MET Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain A residue 511 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 16 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 chunk 23 optimal weight: 0.8980 chunk 34 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 35 optimal weight: 0.9980 chunk 47 optimal weight: 0.2980 chunk 21 optimal weight: 0.4980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3848 r_free = 0.3848 target = 0.153374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.127581 restraints weight = 6669.612| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 2.64 r_work: 0.3409 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.4618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 4375 Z= 0.169 Angle : 0.644 8.382 5978 Z= 0.327 Chirality : 0.042 0.169 653 Planarity : 0.004 0.038 727 Dihedral : 4.775 42.065 576 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 5.23 % Allowed : 19.55 % Favored : 75.23 % 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: 1.48 (0.38), residues: 528 helix: 1.63 (0.27), residues: 371 sheet: None (None), residues: 0 loop : -0.55 (0.55), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 186 TYR 0.014 0.001 TYR A 147 PHE 0.027 0.002 PHE A 263 TRP 0.010 0.001 TRP A 124 HIS 0.002 0.001 HIS A 603 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.17 ( 4374) covalent geometry : angle 0.64444 / 0.33 ( 5976) SS BOND : bond 0.00105 / 0.06 ( 1) SS BOND : angle 0.07018 / 0.04 ( 2) hydrogen bonds : bond 0.04866 / 3.36 ( 293) hydrogen bonds : angle 4.79456 / 3.68 ( 852) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 100 time to evaluate : 0.151 Fit side-chains REVERT: A 338 TYR cc_start: 0.8655 (t80) cc_final: 0.8279 (t80) REVERT: A 430 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.8035 (pp) REVERT: A 519 MET cc_start: 0.7816 (tpp) cc_final: 0.7395 (mmt) REVERT: A 535 PHE cc_start: 0.8084 (t80) cc_final: 0.7790 (t80) REVERT: A 560 MET cc_start: 0.8272 (tpt) cc_final: 0.7348 (ttp) REVERT: A 587 MET cc_start: 0.6065 (ptt) cc_final: 0.5140 (mtt) outliers start: 23 outliers final: 19 residues processed: 111 average time/residue: 0.0479 time to fit residues: 7.6506 Evaluate side-chains 116 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 96 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 TYR Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 313 ILE Chi-restraints excluded: chain A residue 329 SER Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 461 MET Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain A residue 511 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 10 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 11 optimal weight: 0.0050 chunk 20 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 4 optimal weight: 0.6980 chunk 21 optimal weight: 0.1980 chunk 25 optimal weight: 0.8980 chunk 29 optimal weight: 0.9990 overall best weight: 0.5394 ------------------------------------------------------------------------------- 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 = 0.3858 r_free = 0.3858 target = 0.154272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.128437 restraints weight = 6750.893| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 2.67 r_work: 0.3421 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.4772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 4375 Z= 0.153 Angle : 0.649 9.352 5978 Z= 0.327 Chirality : 0.042 0.177 653 Planarity : 0.004 0.037 727 Dihedral : 4.700 42.457 576 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 4.77 % Allowed : 20.23 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.52 (0.38), residues: 528 helix: 1.62 (0.27), residues: 374 sheet: None (None), residues: 0 loop : -0.44 (0.55), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 590 TYR 0.016 0.001 TYR A 542 PHE 0.032 0.002 PHE A 419 TRP 0.010 0.001 TRP A 124 HIS 0.002 0.000 HIS A 603 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.15 ( 4374) covalent geometry : angle 0.64925 / 0.33 ( 5976) SS BOND : bond 0.00126 / 0.07 ( 1) SS BOND : angle 0.10657 / 0.06 ( 2) hydrogen bonds : bond 0.04822 / 3.31 ( 293) hydrogen bonds : angle 4.77540 / 3.63 ( 852) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 106 time to evaluate : 0.165 Fit side-chains REVERT: A 63 MET cc_start: 0.7393 (mtt) cc_final: 0.7083 (ptp) REVERT: A 94 TYR cc_start: 0.8853 (t80) cc_final: 0.8275 (t80) REVERT: A 338 TYR cc_start: 0.8652 (t80) cc_final: 0.8300 (t80) REVERT: A 430 LEU cc_start: 0.8591 (OUTLIER) cc_final: 0.7989 (pp) REVERT: A 519 MET cc_start: 0.7807 (tpp) cc_final: 0.7398 (mmt) REVERT: A 535 PHE cc_start: 0.8023 (t80) cc_final: 0.7751 (t80) REVERT: A 560 MET cc_start: 0.8288 (tpt) cc_final: 0.7369 (ttp) REVERT: A 587 MET cc_start: 0.6115 (ptt) cc_final: 0.5113 (mtt) outliers start: 21 outliers final: 17 residues processed: 116 average time/residue: 0.0416 time to fit residues: 6.9810 Evaluate side-chains 118 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 100 time to evaluate : 0.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 TYR Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 313 ILE Chi-restraints excluded: chain A residue 329 SER Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 461 MET Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain A residue 511 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 46 optimal weight: 0.8980 chunk 39 optimal weight: 0.5980 chunk 28 optimal weight: 0.5980 chunk 15 optimal weight: 3.9990 chunk 21 optimal weight: 0.0670 chunk 27 optimal weight: 0.4980 chunk 48 optimal weight: 0.5980 chunk 10 optimal weight: 0.0870 chunk 22 optimal weight: 0.5980 chunk 9 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 overall best weight: 0.3696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 603 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.156283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.130706 restraints weight = 6650.211| |-----------------------------------------------------------------------------| r_work (start): 0.3575 rms_B_bonded: 2.65 r_work: 0.3455 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.4877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4375 Z= 0.144 Angle : 0.652 9.551 5978 Z= 0.330 Chirality : 0.042 0.170 653 Planarity : 0.004 0.038 727 Dihedral : 4.689 43.598 576 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 4.55 % Allowed : 21.82 % Favored : 73.64 % 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: 1.43 (0.38), residues: 528 helix: 1.56 (0.27), residues: 376 sheet: None (None), residues: 0 loop : -0.51 (0.56), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 514 TYR 0.016 0.001 TYR A 542 PHE 0.032 0.002 PHE A 419 TRP 0.011 0.001 TRP A 154 HIS 0.005 0.001 HIS A 603 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.14 ( 4374) covalent geometry : angle 0.65180 / 0.33 ( 5976) SS BOND : bond 0.00098 / 0.05 ( 1) SS BOND : angle 0.13309 / 0.08 ( 2) hydrogen bonds : bond 0.04766 / 3.26 ( 293) hydrogen bonds : angle 4.81115 / 3.72 ( 852) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 113 time to evaluate : 0.144 Fit side-chains REVERT: A 63 MET cc_start: 0.7436 (mtt) cc_final: 0.7208 (ptp) REVERT: A 94 TYR cc_start: 0.8811 (t80) cc_final: 0.8309 (t80) REVERT: A 338 TYR cc_start: 0.8654 (t80) cc_final: 0.8315 (t80) REVERT: A 519 MET cc_start: 0.7712 (tpp) cc_final: 0.7299 (mmt) REVERT: A 535 PHE cc_start: 0.7970 (t80) cc_final: 0.7692 (t80) REVERT: A 536 ILE cc_start: 0.9022 (mm) cc_final: 0.8682 (mt) REVERT: A 560 MET cc_start: 0.8214 (tpt) cc_final: 0.7354 (ttp) REVERT: A 587 MET cc_start: 0.6089 (ptt) cc_final: 0.5403 (mtt) outliers start: 20 outliers final: 17 residues processed: 124 average time/residue: 0.0375 time to fit residues: 6.6902 Evaluate side-chains 123 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 106 time to evaluate : 0.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 PHE Chi-restraints excluded: chain A residue 80 TYR Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 313 ILE Chi-restraints excluded: chain A residue 329 SER Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 461 MET Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain A residue 511 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 25 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 3 optimal weight: 0.1980 chunk 9 optimal weight: 0.6980 chunk 16 optimal weight: 0.6980 chunk 0 optimal weight: 6.9990 chunk 36 optimal weight: 0.2980 chunk 8 optimal weight: 0.9980 chunk 47 optimal weight: 0.3980 chunk 34 optimal weight: 0.8980 chunk 19 optimal weight: 0.9980 overall best weight: 0.4580 ------------------------------------------------------------------------------- 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 = 0.3790 r_free = 0.3790 target = 0.151943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.126433 restraints weight = 6505.357| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 2.58 r_work: 0.3355 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.5006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 4375 Z= 0.152 Angle : 0.659 9.352 5978 Z= 0.331 Chirality : 0.042 0.173 653 Planarity : 0.004 0.038 727 Dihedral : 4.680 44.182 576 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 4.55 % Allowed : 21.59 % Favored : 73.86 % 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: 1.48 (0.38), residues: 528 helix: 1.59 (0.27), residues: 376 sheet: None (None), residues: 0 loop : -0.48 (0.57), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 514 TYR 0.032 0.001 TYR A 542 PHE 0.034 0.002 PHE A 406 TRP 0.010 0.001 TRP A 154 HIS 0.002 0.000 HIS A 603 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.15 ( 4374) covalent geometry : angle 0.65939 / 0.33 ( 5976) SS BOND : bond 0.00107 / 0.06 ( 1) SS BOND : angle 0.10840 / 0.06 ( 2) hydrogen bonds : bond 0.04749 / 3.25 ( 293) hydrogen bonds : angle 4.76197 / 3.71 ( 852) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 994.95 seconds wall clock time: 17 minutes 45.91 seconds (1065.91 seconds total)