Starting phenix.real_space_refine on Wed Jun 4 22:03:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9krh_62527/06_2025/9krh_62527_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9krh_62527/06_2025/9krh_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_62527/06_2025/9krh_62527.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9krh_62527/06_2025/9krh_62527.map" model { file = "/net/cci-nas-00/data/ceres_data/9krh_62527/06_2025/9krh_62527_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9krh_62527/06_2025/9krh_62527_neut.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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, 11 Unusual residues: {' CL': 1, ' NA': 1, 'CRN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 4.61, per 1000 atoms: 1.09 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: 1.47 Conformation dependent library (CDL) restraints added in 585.2 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: 0.59 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: 1.83 Time building geometry restraints manager: 1.69 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 2.470 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: 15.980 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: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 18.560 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.015 0.002 TRP A 591 HIS 0.004 0.001 HIS A 575 PHE 0.026 0.002 PHE A 68 TYR 0.020 0.001 TYR A 80 ARG 0.002 0.000 ARG A 77 Details of bonding type rmsd hydrogen bonds : bond 0.16201 ( 293) hydrogen bonds : angle 7.11313 ( 852) SS BOND : bond 0.00168 ( 1) SS BOND : angle 1.17877 ( 2) covalent geometry : bond 0.00521 ( 4374) covalent geometry : angle 0.72379 ( 5976) *********************** 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 : 0.582 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: 0.7605 (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: 0.2254 time to fit residues: 49.4186 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 : 0.424 ------------------------------------------------------------------------------- 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 44 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 13 optimal weight: 0.1980 chunk 27 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 30 optimal weight: 0.7980 chunk 48 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 370 GLN A 373 HIS ** A 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.155651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.130307 restraints weight = 6652.295| |-----------------------------------------------------------------------------| r_work (start): 0.3573 rms_B_bonded: 2.55 r_work: 0.3457 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.3137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 4375 Z= 0.186 Angle : 0.657 9.079 5978 Z= 0.343 Chirality : 0.042 0.165 653 Planarity : 0.004 0.031 727 Dihedral : 5.606 57.812 578 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.73 % Allowed : 11.14 % Favored : 86.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.37), residues: 528 helix: 1.28 (0.27), residues: 381 sheet: None (None), residues: 0 loop : -0.74 (0.55), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 591 HIS 0.005 0.001 HIS A 373 PHE 0.020 0.002 PHE A 406 TYR 0.016 0.002 TYR A 542 ARG 0.005 0.001 ARG A 514 Details of bonding type rmsd hydrogen bonds : bond 0.05518 ( 293) hydrogen bonds : angle 5.24876 ( 852) SS BOND : bond 0.00062 ( 1) SS BOND : angle 0.69698 ( 2) covalent geometry : bond 0.00429 ( 4374) covalent geometry : angle 0.65687 ( 5976) *********************** 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 132 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 120 time to evaluate : 0.484 Fit side-chains REVERT: A 245 LEU cc_start: 0.8941 (tt) cc_final: 0.8701 (tt) REVERT: A 369 GLU cc_start: 0.7617 (tm-30) cc_final: 0.7217 (tm-30) REVERT: A 430 LEU cc_start: 0.8885 (OUTLIER) cc_final: 0.8395 (pp) REVERT: A 535 PHE cc_start: 0.8055 (t80) cc_final: 0.7751 (t80) REVERT: A 560 MET cc_start: 0.8040 (tpt) cc_final: 0.7012 (ttt) REVERT: A 587 MET cc_start: 0.6023 (ptt) cc_final: 0.5096 (mtt) outliers start: 12 outliers final: 9 residues processed: 123 average time/residue: 0.1299 time to fit residues: 21.2665 Evaluate side-chains 109 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 99 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 123 VAL 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 415 LEU Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 529 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 13 optimal weight: 0.5980 chunk 10 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 25 optimal weight: 0.6980 chunk 3 optimal weight: 0.6980 chunk 12 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 49 optimal weight: 0.5980 chunk 24 optimal weight: 0.5980 chunk 46 optimal weight: 1.9990 chunk 52 optimal weight: 0.0670 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 603 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.155602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.130297 restraints weight = 6653.042| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 2.55 r_work: 0.3445 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.3545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 4375 Z= 0.154 Angle : 0.591 6.167 5978 Z= 0.309 Chirality : 0.041 0.156 653 Planarity : 0.004 0.034 727 Dihedral : 5.508 59.351 576 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 3.64 % Allowed : 14.32 % Favored : 82.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.38), residues: 528 helix: 1.45 (0.27), residues: 379 sheet: None (None), residues: 0 loop : -0.86 (0.54), residues: 149 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 124 HIS 0.001 0.000 HIS A 174 PHE 0.022 0.002 PHE A 419 TYR 0.017 0.001 TYR A 542 ARG 0.003 0.000 ARG A 514 Details of bonding type rmsd hydrogen bonds : bond 0.04991 ( 293) hydrogen bonds : angle 4.96783 ( 852) SS BOND : bond 0.00167 ( 1) SS BOND : angle 0.47643 ( 2) covalent geometry : bond 0.00353 ( 4374) covalent geometry : angle 0.59119 ( 5976) *********************** 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 133 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 117 time to evaluate : 0.462 Fit side-chains REVERT: A 369 GLU cc_start: 0.7799 (tm-30) cc_final: 0.7380 (tm-30) REVERT: A 430 LEU cc_start: 0.8854 (OUTLIER) cc_final: 0.8350 (pp) REVERT: A 519 MET cc_start: 0.7974 (tpp) cc_final: 0.7320 (mmt) REVERT: A 535 PHE cc_start: 0.8000 (t80) cc_final: 0.7698 (t80) REVERT: A 560 MET cc_start: 0.7945 (tpt) cc_final: 0.7021 (ttm) REVERT: A 587 MET cc_start: 0.6014 (ptt) cc_final: 0.5100 (mtt) outliers start: 16 outliers final: 12 residues processed: 124 average time/residue: 0.1141 time to fit residues: 19.4439 Evaluate side-chains 115 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 102 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 91 LEU 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 227 VAL 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 401 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 16 optimal weight: 0.6980 chunk 20 optimal weight: 0.9980 chunk 24 optimal weight: 0.8980 chunk 32 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 chunk 50 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 ASN A 373 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.152511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.127245 restraints weight = 6621.065| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 2.62 r_work: 0.3390 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.4017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 4375 Z= 0.178 Angle : 0.613 8.521 5978 Z= 0.319 Chirality : 0.042 0.171 653 Planarity : 0.004 0.036 727 Dihedral : 5.256 54.138 576 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 4.32 % Allowed : 16.36 % Favored : 79.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.38), residues: 528 helix: 1.54 (0.27), residues: 377 sheet: None (None), residues: 0 loop : -0.96 (0.54), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 485 HIS 0.004 0.001 HIS A 373 PHE 0.028 0.002 PHE A 263 TYR 0.016 0.001 TYR A 542 ARG 0.002 0.000 ARG A 514 Details of bonding type rmsd hydrogen bonds : bond 0.04879 ( 293) hydrogen bonds : angle 4.87250 ( 852) SS BOND : bond 0.00138 ( 1) SS BOND : angle 0.43388 ( 2) covalent geometry : bond 0.00415 ( 4374) covalent geometry : angle 0.61324 ( 5976) *********************** 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 123 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 104 time to evaluate : 0.417 Fit side-chains REVERT: A 338 TYR cc_start: 0.8445 (t80) cc_final: 0.8043 (t80) REVERT: A 369 GLU cc_start: 0.7774 (tm-30) cc_final: 0.7342 (tm-30) REVERT: A 430 LEU cc_start: 0.8838 (OUTLIER) cc_final: 0.8225 (pp) REVERT: A 519 MET cc_start: 0.7836 (tpp) cc_final: 0.7076 (mmt) REVERT: A 535 PHE cc_start: 0.8067 (t80) cc_final: 0.7748 (t80) REVERT: A 560 MET cc_start: 0.8061 (tpt) cc_final: 0.7115 (ttp) REVERT: A 587 MET cc_start: 0.6001 (ptt) cc_final: 0.5045 (mtt) outliers start: 19 outliers final: 12 residues processed: 110 average time/residue: 0.1131 time to fit residues: 17.1207 Evaluate side-chains 110 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 97 time to evaluate : 0.478 ------------------------------------------------------------------------------- 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 40 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 32 optimal weight: 0.5980 chunk 3 optimal weight: 0.0870 chunk 9 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 chunk 51 optimal weight: 0.5980 chunk 36 optimal weight: 7.9990 chunk 43 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 11 optimal weight: 0.3980 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.154366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.128809 restraints weight = 6731.424| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 2.65 r_work: 0.3357 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.4177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4375 Z= 0.148 Angle : 0.596 9.849 5978 Z= 0.307 Chirality : 0.041 0.149 653 Planarity : 0.004 0.037 727 Dihedral : 5.039 46.573 576 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 4.09 % Allowed : 18.41 % Favored : 77.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.38), residues: 528 helix: 1.60 (0.27), residues: 374 sheet: None (None), residues: 0 loop : -0.57 (0.56), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 402 HIS 0.003 0.001 HIS A 603 PHE 0.025 0.002 PHE A 419 TYR 0.015 0.001 TYR A 147 ARG 0.001 0.000 ARG A 514 Details of bonding type rmsd hydrogen bonds : bond 0.04788 ( 293) hydrogen bonds : angle 4.74666 ( 852) SS BOND : bond 0.00129 ( 1) SS BOND : angle 0.14848 ( 2) covalent geometry : bond 0.00339 ( 4374) covalent geometry : angle 0.59644 ( 5976) *********************** 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 122 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 104 time to evaluate : 0.488 Fit side-chains REVERT: A 338 TYR cc_start: 0.8500 (t80) cc_final: 0.8096 (t80) REVERT: A 369 GLU cc_start: 0.7821 (tm-30) cc_final: 0.7391 (tm-30) REVERT: A 430 LEU cc_start: 0.8795 (OUTLIER) cc_final: 0.8183 (pp) REVERT: A 519 MET cc_start: 0.7786 (tpp) cc_final: 0.7181 (mmt) REVERT: A 535 PHE cc_start: 0.8041 (t80) cc_final: 0.7731 (t80) REVERT: A 536 ILE cc_start: 0.8982 (mm) cc_final: 0.8635 (mt) REVERT: A 560 MET cc_start: 0.8126 (tpt) cc_final: 0.7308 (ttp) REVERT: A 587 MET cc_start: 0.5972 (ptt) cc_final: 0.5020 (mtt) outliers start: 18 outliers final: 14 residues processed: 112 average time/residue: 0.1169 time to fit residues: 18.0694 Evaluate side-chains 116 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 101 time to evaluate : 0.401 ------------------------------------------------------------------------------- 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 372 VAL 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 26 optimal weight: 2.9990 chunk 14 optimal weight: 0.3980 chunk 19 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 27 optimal weight: 0.7980 chunk 51 optimal weight: 0.0980 chunk 29 optimal weight: 0.5980 chunk 39 optimal weight: 0.0970 chunk 9 optimal weight: 0.5980 chunk 2 optimal weight: 0.6980 chunk 7 optimal weight: 2.9990 overall best weight: 0.3578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 373 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.156003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.130081 restraints weight = 6674.132| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 2.66 r_work: 0.3435 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.4402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4375 Z= 0.134 Angle : 0.594 8.925 5978 Z= 0.304 Chirality : 0.041 0.154 653 Planarity : 0.004 0.037 727 Dihedral : 4.870 43.595 576 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 4.55 % Allowed : 20.45 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.56 (0.38), residues: 528 helix: 1.62 (0.27), residues: 379 sheet: None (None), residues: 0 loop : -0.39 (0.57), residues: 149 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 124 HIS 0.004 0.001 HIS A 373 PHE 0.026 0.002 PHE A 419 TYR 0.014 0.001 TYR A 147 ARG 0.002 0.000 ARG A 514 Details of bonding type rmsd hydrogen bonds : bond 0.04680 ( 293) hydrogen bonds : angle 4.69409 ( 852) SS BOND : bond 0.00119 ( 1) SS BOND : angle 0.13440 ( 2) covalent geometry : bond 0.00299 ( 4374) covalent geometry : angle 0.59373 ( 5976) *********************** 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 130 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 110 time to evaluate : 0.440 Fit side-chains REVERT: A 94 TYR cc_start: 0.8820 (t80) cc_final: 0.8167 (t80) REVERT: A 338 TYR cc_start: 0.8603 (t80) cc_final: 0.8255 (t80) REVERT: A 369 GLU cc_start: 0.7833 (tm-30) cc_final: 0.7385 (tm-30) REVERT: A 430 LEU cc_start: 0.8608 (OUTLIER) cc_final: 0.8060 (pp) REVERT: A 490 GLU cc_start: 0.9045 (mm-30) cc_final: 0.8742 (mt-10) REVERT: A 519 MET cc_start: 0.7816 (tpp) cc_final: 0.7225 (mmt) REVERT: A 535 PHE cc_start: 0.8036 (t80) cc_final: 0.7734 (t80) REVERT: A 560 MET cc_start: 0.8262 (tpt) cc_final: 0.7315 (ttp) REVERT: A 587 MET cc_start: 0.5988 (ptt) cc_final: 0.5030 (mtt) outliers start: 20 outliers final: 15 residues processed: 117 average time/residue: 0.1092 time to fit residues: 18.1501 Evaluate side-chains 116 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 100 time to evaluate : 0.441 ------------------------------------------------------------------------------- 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 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 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 42 optimal weight: 2.9990 chunk 9 optimal weight: 0.6980 chunk 30 optimal weight: 0.0050 chunk 31 optimal weight: 0.6980 chunk 4 optimal weight: 0.3980 chunk 39 optimal weight: 0.7980 chunk 0 optimal weight: 6.9990 chunk 47 optimal weight: 0.6980 chunk 13 optimal weight: 0.7980 chunk 11 optimal weight: 0.2980 chunk 33 optimal weight: 0.8980 overall best weight: 0.4194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.155550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.130270 restraints weight = 6669.702| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 2.63 r_work: 0.3446 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.4534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4375 Z= 0.142 Angle : 0.620 10.572 5978 Z= 0.312 Chirality : 0.041 0.172 653 Planarity : 0.004 0.037 727 Dihedral : 4.778 42.002 576 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 5.00 % Allowed : 20.45 % Favored : 74.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.70 (0.38), residues: 528 helix: 1.75 (0.27), residues: 373 sheet: None (None), residues: 0 loop : -0.35 (0.56), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 599 HIS 0.003 0.001 HIS A 603 PHE 0.026 0.002 PHE A 419 TYR 0.015 0.001 TYR A 147 ARG 0.001 0.000 ARG A 514 Details of bonding type rmsd hydrogen bonds : bond 0.04684 ( 293) hydrogen bonds : angle 4.69641 ( 852) SS BOND : bond 0.00135 ( 1) SS BOND : angle 0.13162 ( 2) covalent geometry : bond 0.00326 ( 4374) covalent geometry : angle 0.61976 ( 5976) *********************** 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 126 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 104 time to evaluate : 0.468 Fit side-chains REVERT: A 94 TYR cc_start: 0.8840 (t80) cc_final: 0.8200 (t80) REVERT: A 185 PHE cc_start: 0.7512 (m-80) cc_final: 0.7309 (m-80) REVERT: A 338 TYR cc_start: 0.8649 (t80) cc_final: 0.8296 (t80) REVERT: A 369 GLU cc_start: 0.7801 (tm-30) cc_final: 0.7358 (tm-30) REVERT: A 430 LEU cc_start: 0.8631 (OUTLIER) cc_final: 0.8047 (pp) REVERT: A 490 GLU cc_start: 0.9029 (mm-30) cc_final: 0.8756 (mt-10) REVERT: A 519 MET cc_start: 0.7860 (tpp) cc_final: 0.7341 (mmt) REVERT: A 535 PHE cc_start: 0.8048 (t80) cc_final: 0.7716 (t80) REVERT: A 560 MET cc_start: 0.8367 (tpt) cc_final: 0.7551 (ttp) REVERT: A 587 MET cc_start: 0.6000 (ptt) cc_final: 0.5030 (mtt) outliers start: 22 outliers final: 17 residues processed: 113 average time/residue: 0.1082 time to fit residues: 16.9973 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 : 0.468 ------------------------------------------------------------------------------- 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 0 optimal weight: 7.9990 chunk 7 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 4 optimal weight: 0.6980 chunk 2 optimal weight: 0.8980 chunk 1 optimal weight: 0.9990 chunk 19 optimal weight: 0.5980 chunk 26 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 37 optimal weight: 0.0370 chunk 10 optimal weight: 0.8980 overall best weight: 0.6258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.154309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.129259 restraints weight = 6638.991| |-----------------------------------------------------------------------------| r_work (start): 0.3540 rms_B_bonded: 2.61 r_work: 0.3420 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.4674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 4375 Z= 0.159 Angle : 0.639 9.505 5978 Z= 0.322 Chirality : 0.042 0.169 653 Planarity : 0.004 0.037 727 Dihedral : 4.721 41.043 576 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 5.00 % Allowed : 21.36 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.67 (0.38), residues: 528 helix: 1.70 (0.27), residues: 376 sheet: None (None), residues: 0 loop : -0.30 (0.57), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 485 HIS 0.002 0.001 HIS A 603 PHE 0.026 0.002 PHE A 263 TYR 0.017 0.001 TYR A 147 ARG 0.001 0.000 ARG A 514 Details of bonding type rmsd hydrogen bonds : bond 0.04727 ( 293) hydrogen bonds : angle 4.69388 ( 852) SS BOND : bond 0.00138 ( 1) SS BOND : angle 0.08869 ( 2) covalent geometry : bond 0.00373 ( 4374) covalent geometry : angle 0.63886 ( 5976) *********************** 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 126 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 104 time to evaluate : 0.431 Fit side-chains REVERT: A 338 TYR cc_start: 0.8583 (t80) cc_final: 0.8283 (t80) REVERT: A 369 GLU cc_start: 0.7841 (tm-30) cc_final: 0.7394 (tm-30) REVERT: A 430 LEU cc_start: 0.8581 (OUTLIER) cc_final: 0.7992 (pp) REVERT: A 490 GLU cc_start: 0.9046 (mm-30) cc_final: 0.8812 (mt-10) REVERT: A 519 MET cc_start: 0.7821 (tpp) cc_final: 0.7322 (mmt) REVERT: A 535 PHE cc_start: 0.8078 (t80) cc_final: 0.7732 (t80) REVERT: A 560 MET cc_start: 0.8426 (tpt) cc_final: 0.7453 (ttp) REVERT: A 587 MET cc_start: 0.6076 (ptt) cc_final: 0.5107 (mtt) outliers start: 22 outliers final: 17 residues processed: 116 average time/residue: 0.1037 time to fit residues: 16.9134 Evaluate side-chains 119 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 101 time to evaluate : 0.431 ------------------------------------------------------------------------------- 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 37 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 chunk 8 optimal weight: 0.6980 chunk 7 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 chunk 38 optimal weight: 0.9980 chunk 10 optimal weight: 0.4980 chunk 6 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.153370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.127858 restraints weight = 6657.129| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 2.63 r_work: 0.3289 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.4775 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= 0.167 Angle : 0.650 9.244 5978 Z= 0.329 Chirality : 0.042 0.178 653 Planarity : 0.004 0.035 727 Dihedral : 4.707 39.220 576 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 4.09 % Allowed : 22.50 % Favored : 73.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.38), residues: 528 helix: 1.59 (0.27), residues: 379 sheet: None (None), residues: 0 loop : -0.32 (0.58), residues: 149 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 154 HIS 0.002 0.001 HIS A 603 PHE 0.031 0.002 PHE A 419 TYR 0.017 0.001 TYR A 147 ARG 0.001 0.000 ARG A 514 Details of bonding type rmsd hydrogen bonds : bond 0.04865 ( 293) hydrogen bonds : angle 4.76889 ( 852) SS BOND : bond 0.00091 ( 1) SS BOND : angle 0.49379 ( 2) covalent geometry : bond 0.00392 ( 4374) covalent geometry : angle 0.65030 ( 5976) *********************** 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 132 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 114 time to evaluate : 0.428 Fit side-chains REVERT: A 63 MET cc_start: 0.7418 (mtt) cc_final: 0.7107 (ptp) REVERT: A 338 TYR cc_start: 0.8658 (t80) cc_final: 0.8292 (t80) REVERT: A 369 GLU cc_start: 0.7840 (tm-30) cc_final: 0.7385 (tm-30) REVERT: A 430 LEU cc_start: 0.8617 (OUTLIER) cc_final: 0.8003 (pp) REVERT: A 519 MET cc_start: 0.7854 (tpp) cc_final: 0.7386 (mmt) REVERT: A 535 PHE cc_start: 0.8051 (t80) cc_final: 0.7725 (t80) REVERT: A 560 MET cc_start: 0.8393 (tpt) cc_final: 0.7462 (ttp) REVERT: A 587 MET cc_start: 0.6084 (ptt) cc_final: 0.5161 (mtt) outliers start: 18 outliers final: 17 residues processed: 123 average time/residue: 0.1044 time to fit residues: 17.8190 Evaluate side-chains 122 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 104 time to evaluate : 0.430 ------------------------------------------------------------------------------- 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 123 VAL Chi-restraints excluded: chain A residue 164 THR 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 42 optimal weight: 0.6980 chunk 41 optimal weight: 0.5980 chunk 21 optimal weight: 0.0980 chunk 48 optimal weight: 0.6980 chunk 26 optimal weight: 0.9990 chunk 46 optimal weight: 0.9990 chunk 2 optimal weight: 0.8980 chunk 37 optimal weight: 0.9990 chunk 1 optimal weight: 0.7980 chunk 7 optimal weight: 0.3980 chunk 20 optimal weight: 0.8980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3864 r_free = 0.3864 target = 0.154836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.129137 restraints weight = 6600.498| |-----------------------------------------------------------------------------| r_work (start): 0.3560 rms_B_bonded: 2.63 r_work: 0.3444 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.4962 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= 0.152 Angle : 0.665 9.429 5978 Z= 0.334 Chirality : 0.042 0.165 653 Planarity : 0.004 0.036 727 Dihedral : 4.661 37.095 576 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 13.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 4.09 % Allowed : 23.41 % Favored : 72.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (0.38), residues: 528 helix: 1.59 (0.27), residues: 376 sheet: None (None), residues: 0 loop : -0.43 (0.56), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 124 HIS 0.006 0.001 HIS A 603 PHE 0.037 0.002 PHE A 263 TYR 0.017 0.001 TYR A 147 ARG 0.002 0.000 ARG A 443 Details of bonding type rmsd hydrogen bonds : bond 0.04777 ( 293) hydrogen bonds : angle 4.76954 ( 852) SS BOND : bond 0.00269 ( 1) SS BOND : angle 0.36107 ( 2) covalent geometry : bond 0.00355 ( 4374) covalent geometry : angle 0.66513 ( 5976) ********************** 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 119 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 101 time to evaluate : 0.442 Fit side-chains REVERT: A 63 MET cc_start: 0.7421 (mtt) cc_final: 0.7104 (ptp) REVERT: A 338 TYR cc_start: 0.8568 (t80) cc_final: 0.8187 (t80) REVERT: A 369 GLU cc_start: 0.7835 (tm-30) cc_final: 0.7382 (tm-30) REVERT: A 519 MET cc_start: 0.7793 (tpp) cc_final: 0.7333 (mmt) REVERT: A 535 PHE cc_start: 0.8069 (t80) cc_final: 0.7764 (t80) REVERT: A 560 MET cc_start: 0.8397 (tpt) cc_final: 0.7460 (ttp) REVERT: A 587 MET cc_start: 0.6015 (ptt) cc_final: 0.5410 (mtt) outliers start: 18 outliers final: 17 residues processed: 110 average time/residue: 0.1061 time to fit residues: 16.4013 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 : 0.443 ------------------------------------------------------------------------------- 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 123 VAL Chi-restraints excluded: chain A residue 164 THR 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 415 LEU 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 15 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 chunk 6 optimal weight: 0.0570 chunk 34 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 chunk 48 optimal weight: 0.7980 chunk 28 optimal weight: 0.9990 chunk 32 optimal weight: 0.3980 chunk 47 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 22 optimal weight: 0.5980 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 603 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.150472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.124359 restraints weight = 6483.752| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 2.68 r_work: 0.3333 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.4963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 4375 Z= 0.157 Angle : 0.664 9.110 5978 Z= 0.333 Chirality : 0.042 0.172 653 Planarity : 0.004 0.037 727 Dihedral : 4.633 36.314 576 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 3.86 % Allowed : 23.41 % Favored : 72.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.38), residues: 528 helix: 1.55 (0.27), residues: 379 sheet: None (None), residues: 0 loop : -0.41 (0.57), residues: 149 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 124 HIS 0.003 0.001 HIS A 603 PHE 0.037 0.002 PHE A 406 TYR 0.016 0.001 TYR A 147 ARG 0.004 0.000 ARG A 590 Details of bonding type rmsd hydrogen bonds : bond 0.04776 ( 293) hydrogen bonds : angle 4.70045 ( 852) SS BOND : bond 0.00228 ( 1) SS BOND : angle 0.34178 ( 2) covalent geometry : bond 0.00366 ( 4374) covalent geometry : angle 0.66409 ( 5976) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2445.00 seconds wall clock time: 43 minutes 18.67 seconds (2598.67 seconds total)