Starting phenix.real_space_refine on Tue Feb 3 13:22:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7n5f_24188/02_2026/7n5f_24188.cif Found real_map, /net/cci-nas-00/data/ceres_data/7n5f_24188/02_2026/7n5f_24188.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7n5f_24188/02_2026/7n5f_24188.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7n5f_24188/02_2026/7n5f_24188.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7n5f_24188/02_2026/7n5f_24188.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7n5f_24188/02_2026/7n5f_24188.map" } resolution = 2.7 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= 0.001 sd= 0.027 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 12 5.16 5 C 1996 2.51 5 N 503 2.21 5 O 526 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3037 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3019 Number of conformers: 1 Conformer: "" Number of residues, atoms: 386, 3019 Classifications: {'peptide': 386} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 7, 'TRANS': 378} Chain breaks: 5 Unresolved non-hydrogen bonds: 133 Unresolved non-hydrogen angles: 177 Unresolved non-hydrogen dihedrals: 113 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'GLU:plan': 1, 'PHE:plan': 3, 'TRP:plan': 2, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 50 Chain: "A" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 18 Unusual residues: {'PLM': 1} Classifications: {'undetermined': 1} Time building chain proxies: 0.91, per 1000 atoms: 0.30 Number of scatterers: 3037 At special positions: 0 Unit cell: (56.65, 90.64, 141.11, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 12 16.00 O 526 8.00 N 503 7.00 C 1996 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.28 Conformation dependent library (CDL) restraints added in 114.6 milliseconds 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 746 Finding SS restraints... Secondary structure from input PDB file: 13 helices and 2 sheets defined 64.8% alpha, 12.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.10 Creating SS restraints... Processing helix chain 'A' and resid 186 through 189 Processing helix chain 'A' and resid 190 through 200 Processing helix chain 'A' and resid 224 through 231 removed outlier: 3.854A pdb=" N SER A 231 " --> pdb=" O LEU A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 244 Processing helix chain 'A' and resid 259 through 283 removed outlier: 5.237A pdb=" N THR A 266 " --> pdb=" O HIS A 262 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N SER A 267 " --> pdb=" O GLY A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 333 removed outlier: 4.266A pdb=" N HIS A 331 " --> pdb=" O ALA A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 353 Processing helix chain 'A' and resid 504 through 552 Processing helix chain 'A' and resid 556 through 574 removed outlier: 3.585A pdb=" N PHE A 572 " --> pdb=" O VAL A 568 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 590 Processing helix chain 'A' and resid 631 through 635 Processing helix chain 'A' and resid 661 through 678 Processing helix chain 'A' and resid 714 through 737 Processing sheet with id=AA1, first strand: chain 'A' and resid 626 through 630 removed outlier: 7.273A pdb=" N THR A 616 " --> pdb=" O MET A 612 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N MET A 612 " --> pdb=" O THR A 616 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N VAL A 618 " --> pdb=" O GLU A 610 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 649 through 657 removed outlier: 6.531A pdb=" N LYS A 699 " --> pdb=" O ILE A 694 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N ILE A 694 " --> pdb=" O LYS A 699 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N LYS A 701 " --> pdb=" O LYS A 692 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ASN A 707 " --> pdb=" O GLN A 686 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N GLN A 686 " --> pdb=" O ASN A 707 " (cutoff:3.500A) 220 hydrogen bonds defined for protein. 654 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: 0.45 Time building geometry restraints manager: 0.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 566 1.31 - 1.44: 824 1.44 - 1.56: 1667 1.56 - 1.69: 16 1.69 - 1.82: 21 Bond restraints: 3094 Sorted by residual: bond pdb=" CB HIS A 331 " pdb=" CG HIS A 331 " ideal model delta sigma weight residual 1.497 1.404 0.093 1.40e-02 5.10e+03 4.39e+01 bond pdb=" CB ILE A 285 " pdb=" CG1 ILE A 285 " ideal model delta sigma weight residual 1.530 1.654 -0.124 2.00e-02 2.50e+03 3.86e+01 bond pdb=" NE1 TRP A 273 " pdb=" CE2 TRP A 273 " ideal model delta sigma weight residual 1.370 1.315 0.055 1.10e-02 8.26e+03 2.52e+01 bond pdb=" CB LEU A 258 " pdb=" CG LEU A 258 " ideal model delta sigma weight residual 1.530 1.628 -0.098 2.00e-02 2.50e+03 2.38e+01 bond pdb=" CB TYR A 629 " pdb=" CG TYR A 629 " ideal model delta sigma weight residual 1.512 1.406 0.106 2.20e-02 2.07e+03 2.34e+01 ... (remaining 3089 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.65: 3277 1.65 - 3.31: 716 3.31 - 4.96: 159 4.96 - 6.61: 32 6.61 - 8.27: 6 Bond angle restraints: 4190 Sorted by residual: angle pdb=" CA PHE A 335 " pdb=" CB PHE A 335 " pdb=" CG PHE A 335 " ideal model delta sigma weight residual 113.80 122.07 -8.27 1.00e+00 1.00e+00 6.83e+01 angle pdb=" C LEU A 743 " pdb=" N PRO A 744 " pdb=" CA PRO A 744 " ideal model delta sigma weight residual 119.85 126.24 -6.39 1.01e+00 9.80e-01 4.00e+01 angle pdb=" C HIS A 592 " pdb=" N PRO A 593 " pdb=" CA PRO A 593 " ideal model delta sigma weight residual 119.56 125.29 -5.73 1.01e+00 9.80e-01 3.22e+01 angle pdb=" C SER A 645 " pdb=" N PRO A 646 " pdb=" CA PRO A 646 " ideal model delta sigma weight residual 120.98 126.89 -5.91 1.07e+00 8.73e-01 3.05e+01 angle pdb=" C TYR A 629 " pdb=" N PRO A 630 " pdb=" CA PRO A 630 " ideal model delta sigma weight residual 119.76 125.32 -5.56 1.03e+00 9.43e-01 2.91e+01 ... (remaining 4185 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.70: 1782 17.70 - 35.40: 36 35.40 - 53.09: 8 53.09 - 70.79: 2 70.79 - 88.49: 3 Dihedral angle restraints: 1831 sinusoidal: 699 harmonic: 1132 Sorted by residual: dihedral pdb=" N PHE A 335 " pdb=" C PHE A 335 " pdb=" CA PHE A 335 " pdb=" CB PHE A 335 " ideal model delta harmonic sigma weight residual 122.80 130.99 -8.19 0 2.50e+00 1.60e-01 1.07e+01 dihedral pdb=" N ARG A 296 " pdb=" C ARG A 296 " pdb=" CA ARG A 296 " pdb=" CB ARG A 296 " ideal model delta harmonic sigma weight residual 122.80 114.65 8.15 0 2.50e+00 1.60e-01 1.06e+01 dihedral pdb=" CB GLU A 611 " pdb=" CG GLU A 611 " pdb=" CD GLU A 611 " pdb=" OE1 GLU A 611 " ideal model delta sinusoidal sigma weight residual 0.00 -88.49 88.49 1 3.00e+01 1.11e-03 1.04e+01 ... (remaining 1828 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.108: 408 0.108 - 0.216: 84 0.216 - 0.323: 12 0.323 - 0.431: 0 0.431 - 0.539: 2 Chirality restraints: 506 Sorted by residual: chirality pdb=" CB ILE A 285 " pdb=" CA ILE A 285 " pdb=" CG1 ILE A 285 " pdb=" CG2 ILE A 285 " both_signs ideal model delta sigma weight residual False 2.64 3.18 -0.54 2.00e-01 2.50e+01 7.25e+00 chirality pdb=" CG LEU A 258 " pdb=" CB LEU A 258 " pdb=" CD1 LEU A 258 " pdb=" CD2 LEU A 258 " both_signs ideal model delta sigma weight residual False -2.59 -3.12 0.53 2.00e-01 2.50e+01 7.01e+00 chirality pdb=" CA PHE A 335 " pdb=" N PHE A 335 " pdb=" C PHE A 335 " pdb=" CB PHE A 335 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.58e+00 ... (remaining 503 not shown) Planarity restraints: 511 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 335 " -0.059 2.00e-02 2.50e+03 3.66e-02 2.35e+01 pdb=" CG PHE A 335 " 0.057 2.00e-02 2.50e+03 pdb=" CD1 PHE A 335 " 0.022 2.00e-02 2.50e+03 pdb=" CD2 PHE A 335 " 0.031 2.00e-02 2.50e+03 pdb=" CE1 PHE A 335 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE A 335 " -0.013 2.00e-02 2.50e+03 pdb=" CZ PHE A 335 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 697 " 0.016 2.00e-02 2.50e+03 3.16e-02 9.99e+00 pdb=" C VAL A 697 " -0.055 2.00e-02 2.50e+03 pdb=" O VAL A 697 " 0.021 2.00e-02 2.50e+03 pdb=" N ASN A 698 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 329 " -0.015 2.00e-02 2.50e+03 2.96e-02 8.78e+00 pdb=" C SER A 329 " 0.051 2.00e-02 2.50e+03 pdb=" O SER A 329 " -0.019 2.00e-02 2.50e+03 pdb=" N PHE A 330 " -0.017 2.00e-02 2.50e+03 ... (remaining 508 not shown) Histogram of nonbonded interaction distances: 2.47 - 2.95: 1532 2.95 - 3.44: 3149 3.44 - 3.93: 4806 3.93 - 4.41: 5610 4.41 - 4.90: 8455 Nonbonded interactions: 23552 Sorted by model distance: nonbonded pdb=" N ASN A 711 " pdb=" O ASN A 711 " model vdw 2.468 2.496 nonbonded pdb=" NZ LYS A 730 " pdb=" OE2 GLU A 734 " model vdw 2.473 3.120 nonbonded pdb=" N VAL A 697 " pdb=" N ASN A 698 " model vdw 2.491 2.560 nonbonded pdb=" NZ LYS A 579 " pdb=" OE2 GLU A 583 " model vdw 2.506 3.120 nonbonded pdb=" N THR A 295 " pdb=" N ARG A 296 " model vdw 2.536 2.560 ... (remaining 23547 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: 1.460 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: 0.070 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 5.350 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7244 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 : 0.023 0.124 3094 Z= 1.242 Angle : 1.502 8.265 4190 Z= 1.032 Chirality : 0.097 0.539 506 Planarity : 0.008 0.037 511 Dihedral : 9.991 88.488 1085 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 0.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % 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: 1.68 (0.40), residues: 374 helix: 1.43 (0.29), residues: 242 sheet: 0.14 (0.80), residues: 38 loop : 1.02 (0.67), residues: 94 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 334 TYR 0.026 0.006 TYR A 675 PHE 0.059 0.006 PHE A 335 TRP 0.025 0.007 TRP A 622 HIS 0.009 0.003 HIS A 331 Details of bonding type rmsd covalent geometry : bond 0.02272 ( 3094) covalent geometry : angle 1.50169 ( 4190) hydrogen bonds : bond 0.14783 ( 220) hydrogen bonds : angle 6.03866 ( 654) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 152 time to evaluate : 0.115 Fit side-chains REVERT: A 350 GLN cc_start: 0.7950 (mt0) cc_final: 0.7715 (mt0) REVERT: A 548 TRP cc_start: 0.8678 (t60) cc_final: 0.8248 (t60) REVERT: A 591 MET cc_start: 0.7817 (mtp) cc_final: 0.7552 (mtp) REVERT: A 624 LYS cc_start: 0.8809 (mmtp) cc_final: 0.7292 (tmmt) REVERT: A 655 SER cc_start: 0.8107 (p) cc_final: 0.7870 (m) REVERT: A 675 TYR cc_start: 0.8227 (t80) cc_final: 0.7893 (t80) outliers start: 0 outliers final: 0 residues processed: 152 average time/residue: 0.4496 time to fit residues: 70.3268 Evaluate side-chains 133 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 0.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 24 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 32 optimal weight: 0.9980 chunk 31 optimal weight: 0.6980 chunk 25 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 22 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 648 GLN A 698 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.153979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.137341 restraints weight = 4642.808| |-----------------------------------------------------------------------------| r_work (start): 0.3915 rms_B_bonded: 2.03 r_work: 0.3795 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3641 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.2855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 3094 Z= 0.169 Angle : 0.559 6.098 4190 Z= 0.313 Chirality : 0.042 0.144 506 Planarity : 0.004 0.028 511 Dihedral : 5.899 47.598 411 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Rotamer: Outliers : 3.81 % Allowed : 18.73 % Favored : 77.46 % 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: 3.38 (0.45), residues: 374 helix: 2.94 (0.32), residues: 232 sheet: 0.60 (0.72), residues: 44 loop : 1.41 (0.80), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 720 TYR 0.010 0.001 TYR A 675 PHE 0.015 0.002 PHE A 335 TRP 0.012 0.002 TRP A 304 HIS 0.008 0.002 HIS A 331 Details of bonding type rmsd covalent geometry : bond 0.00362 ( 3094) covalent geometry : angle 0.55937 ( 4190) hydrogen bonds : bond 0.06064 ( 220) hydrogen bonds : angle 4.18890 ( 654) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 125 time to evaluate : 0.072 Fit side-chains REVERT: A 261 THR cc_start: 0.7268 (m) cc_final: 0.7056 (p) REVERT: A 576 ASN cc_start: 0.7610 (t0) cc_final: 0.7333 (t0) REVERT: A 624 LYS cc_start: 0.8811 (mmtp) cc_final: 0.6741 (tmmt) REVERT: A 626 LYS cc_start: 0.6434 (OUTLIER) cc_final: 0.4240 (mptp) REVERT: A 655 SER cc_start: 0.8663 (p) cc_final: 0.8327 (m) REVERT: A 728 GLU cc_start: 0.7434 (tp30) cc_final: 0.7221 (tp30) outliers start: 12 outliers final: 3 residues processed: 129 average time/residue: 0.3847 time to fit residues: 51.1213 Evaluate side-chains 126 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 122 time to evaluate : 0.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 626 LYS Chi-restraints excluded: chain A residue 632 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 28 optimal weight: 3.9990 chunk 26 optimal weight: 0.9990 chunk 10 optimal weight: 0.7980 chunk 8 optimal weight: 0.6980 chunk 7 optimal weight: 0.9980 chunk 37 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 18 optimal weight: 0.7980 chunk 6 optimal weight: 4.9990 chunk 27 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 648 GLN A 698 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.153917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.136688 restraints weight = 4604.555| |-----------------------------------------------------------------------------| r_work (start): 0.3905 rms_B_bonded: 1.99 r_work: 0.3784 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3629 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.3640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3094 Z= 0.144 Angle : 0.489 7.266 4190 Z= 0.277 Chirality : 0.042 0.143 506 Planarity : 0.003 0.029 511 Dihedral : 5.559 44.820 411 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 6.67 % Allowed : 22.54 % Favored : 70.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 3.30 (0.45), residues: 374 helix: 2.93 (0.32), residues: 233 sheet: 0.84 (0.75), residues: 44 loop : 1.06 (0.79), residues: 97 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 721 TYR 0.010 0.001 TYR A 675 PHE 0.028 0.002 PHE A 344 TRP 0.014 0.002 TRP A 316 HIS 0.005 0.002 HIS A 592 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 3094) covalent geometry : angle 0.48940 ( 4190) hydrogen bonds : bond 0.05002 ( 220) hydrogen bonds : angle 3.98079 ( 654) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 118 time to evaluate : 0.071 Fit side-chains REVERT: A 576 ASN cc_start: 0.7647 (t0) cc_final: 0.7356 (t0) REVERT: A 624 LYS cc_start: 0.8845 (mmtp) cc_final: 0.6784 (tmmt) REVERT: A 626 LYS cc_start: 0.6406 (OUTLIER) cc_final: 0.4274 (mptp) REVERT: A 655 SER cc_start: 0.8652 (p) cc_final: 0.8364 (m) REVERT: A 689 MET cc_start: 0.8500 (OUTLIER) cc_final: 0.8286 (mmm) REVERT: A 699 LYS cc_start: 0.8358 (ttpp) cc_final: 0.8095 (ttmt) REVERT: A 737 ASP cc_start: 0.7894 (t0) cc_final: 0.7690 (t0) outliers start: 21 outliers final: 7 residues processed: 125 average time/residue: 0.3729 time to fit residues: 48.0488 Evaluate side-chains 124 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 115 time to evaluate : 0.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 296 ARG Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 583 GLU Chi-restraints excluded: chain A residue 626 LYS Chi-restraints excluded: chain A residue 689 MET Chi-restraints excluded: chain A residue 724 GLU Chi-restraints excluded: chain A residue 748 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 16 optimal weight: 0.7980 chunk 34 optimal weight: 0.0070 chunk 22 optimal weight: 0.8980 chunk 9 optimal weight: 0.8980 chunk 2 optimal weight: 9.9990 chunk 0 optimal weight: 8.9990 chunk 8 optimal weight: 0.7980 chunk 24 optimal weight: 0.8980 chunk 23 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 overall best weight: 0.6798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 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 = 0.4136 r_free = 0.4136 target = 0.154038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.136807 restraints weight = 4617.243| |-----------------------------------------------------------------------------| r_work (start): 0.3909 rms_B_bonded: 2.00 r_work: 0.3789 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3633 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.3919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3094 Z= 0.130 Angle : 0.473 5.304 4190 Z= 0.267 Chirality : 0.041 0.154 506 Planarity : 0.003 0.030 511 Dihedral : 5.470 44.234 411 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 6.03 % Allowed : 24.76 % Favored : 69.21 % 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: 3.38 (0.46), residues: 374 helix: 3.04 (0.33), residues: 233 sheet: 0.87 (0.77), residues: 44 loop : 0.93 (0.78), residues: 97 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 720 TYR 0.018 0.002 TYR A 675 PHE 0.019 0.002 PHE A 271 TRP 0.016 0.002 TRP A 316 HIS 0.006 0.002 HIS A 592 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 3094) covalent geometry : angle 0.47322 ( 4190) hydrogen bonds : bond 0.04668 ( 220) hydrogen bonds : angle 3.89617 ( 654) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 118 time to evaluate : 0.121 Fit side-chains REVERT: A 535 LEU cc_start: 0.8701 (tm) cc_final: 0.8491 (tp) REVERT: A 576 ASN cc_start: 0.7653 (t0) cc_final: 0.7421 (t0) REVERT: A 582 PHE cc_start: 0.8002 (t80) cc_final: 0.7695 (t80) REVERT: A 624 LYS cc_start: 0.8838 (mmtp) cc_final: 0.6789 (tmmt) REVERT: A 626 LYS cc_start: 0.6426 (OUTLIER) cc_final: 0.4161 (mptp) REVERT: A 655 SER cc_start: 0.8666 (p) cc_final: 0.8371 (m) REVERT: A 689 MET cc_start: 0.8512 (OUTLIER) cc_final: 0.8245 (mmm) REVERT: A 737 ASP cc_start: 0.7922 (t0) cc_final: 0.7671 (t0) outliers start: 19 outliers final: 8 residues processed: 125 average time/residue: 0.3889 time to fit residues: 50.0883 Evaluate side-chains 128 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 118 time to evaluate : 0.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 296 ARG Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 543 MET Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 583 GLU Chi-restraints excluded: chain A residue 626 LYS Chi-restraints excluded: chain A residue 689 MET Chi-restraints excluded: chain A residue 724 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 33 optimal weight: 3.9990 chunk 2 optimal weight: 8.9990 chunk 17 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 10 optimal weight: 0.8980 chunk 16 optimal weight: 0.8980 chunk 12 optimal weight: 0.8980 chunk 14 optimal weight: 0.7980 chunk 20 optimal weight: 3.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 648 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.153197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.135895 restraints weight = 4615.417| |-----------------------------------------------------------------------------| r_work (start): 0.3896 rms_B_bonded: 2.00 r_work: 0.3777 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3624 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.4136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3094 Z= 0.148 Angle : 0.473 5.152 4190 Z= 0.267 Chirality : 0.042 0.169 506 Planarity : 0.003 0.030 511 Dihedral : 5.368 41.026 411 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 8.25 % Allowed : 22.22 % Favored : 69.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 3.21 (0.45), residues: 374 helix: 3.02 (0.32), residues: 233 sheet: 0.77 (0.75), residues: 44 loop : 0.54 (0.75), residues: 97 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 296 TYR 0.022 0.002 TYR A 675 PHE 0.018 0.002 PHE A 344 TRP 0.011 0.001 TRP A 316 HIS 0.006 0.002 HIS A 592 Details of bonding type rmsd covalent geometry : bond 0.00328 ( 3094) covalent geometry : angle 0.47283 ( 4190) hydrogen bonds : bond 0.04616 ( 220) hydrogen bonds : angle 3.85911 ( 654) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 121 time to evaluate : 0.074 Fit side-chains REVERT: A 316 TRP cc_start: 0.8395 (OUTLIER) cc_final: 0.7029 (t60) REVERT: A 573 ILE cc_start: 0.8285 (OUTLIER) cc_final: 0.8083 (mp) REVERT: A 576 ASN cc_start: 0.7604 (t0) cc_final: 0.7367 (t0) REVERT: A 582 PHE cc_start: 0.8016 (t80) cc_final: 0.7565 (t80) REVERT: A 624 LYS cc_start: 0.8831 (mmtp) cc_final: 0.6814 (tmmt) REVERT: A 626 LYS cc_start: 0.6446 (OUTLIER) cc_final: 0.4197 (mptp) REVERT: A 655 SER cc_start: 0.8666 (p) cc_final: 0.8391 (m) REVERT: A 689 MET cc_start: 0.8527 (tpp) cc_final: 0.8296 (mmm) REVERT: A 737 ASP cc_start: 0.7997 (t0) cc_final: 0.7667 (t0) outliers start: 26 outliers final: 11 residues processed: 126 average time/residue: 0.4413 time to fit residues: 57.0987 Evaluate side-chains 134 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 120 time to evaluate : 0.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 296 ARG Chi-restraints excluded: chain A residue 301 PHE Chi-restraints excluded: chain A residue 316 TRP Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 541 ILE Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 583 GLU Chi-restraints excluded: chain A residue 607 MET Chi-restraints excluded: chain A residue 626 LYS Chi-restraints excluded: chain A residue 645 SER Chi-restraints excluded: chain A residue 748 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 3 optimal weight: 0.2980 chunk 29 optimal weight: 0.6980 chunk 37 optimal weight: 2.9990 chunk 5 optimal weight: 0.6980 chunk 7 optimal weight: 4.9990 chunk 36 optimal weight: 0.6980 chunk 9 optimal weight: 0.7980 chunk 28 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 27 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 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 = 0.4138 r_free = 0.4138 target = 0.154291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.136827 restraints weight = 4570.958| |-----------------------------------------------------------------------------| r_work (start): 0.3908 rms_B_bonded: 2.00 r_work: 0.3790 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3637 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.4317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3094 Z= 0.123 Angle : 0.473 6.618 4190 Z= 0.260 Chirality : 0.041 0.170 506 Planarity : 0.003 0.030 511 Dihedral : 5.689 53.319 411 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 5.40 % Allowed : 27.30 % Favored : 67.30 % 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: 3.25 (0.46), residues: 374 helix: 3.07 (0.33), residues: 233 sheet: 0.76 (0.77), residues: 44 loop : 0.50 (0.76), residues: 97 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 671 TYR 0.022 0.002 TYR A 675 PHE 0.017 0.002 PHE A 344 TRP 0.011 0.001 TRP A 316 HIS 0.005 0.001 HIS A 592 Details of bonding type rmsd covalent geometry : bond 0.00263 ( 3094) covalent geometry : angle 0.47289 ( 4190) hydrogen bonds : bond 0.04351 ( 220) hydrogen bonds : angle 3.75463 ( 654) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 122 time to evaluate : 0.092 Fit side-chains REVERT: A 316 TRP cc_start: 0.8388 (OUTLIER) cc_final: 0.6884 (t60) REVERT: A 522 LEU cc_start: 0.8776 (mm) cc_final: 0.8554 (mp) REVERT: A 535 LEU cc_start: 0.8678 (tm) cc_final: 0.8419 (tp) REVERT: A 576 ASN cc_start: 0.7604 (t0) cc_final: 0.7387 (t0) REVERT: A 581 ILE cc_start: 0.7948 (mm) cc_final: 0.7685 (mp) REVERT: A 582 PHE cc_start: 0.8042 (t80) cc_final: 0.7633 (t80) REVERT: A 610 GLU cc_start: 0.7560 (OUTLIER) cc_final: 0.7338 (mm-30) REVERT: A 624 LYS cc_start: 0.8806 (mmtp) cc_final: 0.6811 (tmmt) REVERT: A 626 LYS cc_start: 0.6400 (OUTLIER) cc_final: 0.4139 (mptp) REVERT: A 655 SER cc_start: 0.8667 (p) cc_final: 0.8392 (m) REVERT: A 678 GLN cc_start: 0.8016 (mm-40) cc_final: 0.7811 (mm-40) REVERT: A 689 MET cc_start: 0.8540 (OUTLIER) cc_final: 0.8325 (mmm) REVERT: A 737 ASP cc_start: 0.7990 (t0) cc_final: 0.7646 (t0) outliers start: 17 outliers final: 6 residues processed: 125 average time/residue: 0.3349 time to fit residues: 43.1728 Evaluate side-chains 130 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 120 time to evaluate : 0.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 296 ARG Chi-restraints excluded: chain A residue 316 TRP Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 610 GLU Chi-restraints excluded: chain A residue 626 LYS Chi-restraints excluded: chain A residue 689 MET Chi-restraints excluded: chain A residue 748 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 31 optimal weight: 2.9990 chunk 27 optimal weight: 0.5980 chunk 33 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 16 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 35 optimal weight: 0.6980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 513 ASN A 648 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.153185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.135916 restraints weight = 4654.556| |-----------------------------------------------------------------------------| r_work (start): 0.3898 rms_B_bonded: 2.00 r_work: 0.3775 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3618 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.4419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 3094 Z= 0.165 Angle : 0.496 5.871 4190 Z= 0.277 Chirality : 0.043 0.175 506 Planarity : 0.003 0.030 511 Dihedral : 5.692 59.980 411 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 6.35 % Allowed : 26.03 % Favored : 67.62 % 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: 3.05 (0.45), residues: 374 helix: 2.94 (0.33), residues: 233 sheet: 0.69 (0.77), residues: 44 loop : 0.37 (0.75), residues: 97 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 334 TYR 0.023 0.002 TYR A 675 PHE 0.019 0.002 PHE A 330 TRP 0.008 0.001 TRP A 683 HIS 0.006 0.001 HIS A 592 Details of bonding type rmsd covalent geometry : bond 0.00378 ( 3094) covalent geometry : angle 0.49628 ( 4190) hydrogen bonds : bond 0.04711 ( 220) hydrogen bonds : angle 3.88971 ( 654) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 121 time to evaluate : 0.114 Fit side-chains REVERT: A 316 TRP cc_start: 0.8446 (OUTLIER) cc_final: 0.6798 (t60) REVERT: A 535 LEU cc_start: 0.8703 (tm) cc_final: 0.8479 (tp) REVERT: A 581 ILE cc_start: 0.8002 (mm) cc_final: 0.7755 (mp) REVERT: A 582 PHE cc_start: 0.7999 (t80) cc_final: 0.7579 (t80) REVERT: A 610 GLU cc_start: 0.7584 (OUTLIER) cc_final: 0.7363 (mm-30) REVERT: A 624 LYS cc_start: 0.8807 (mmtp) cc_final: 0.6845 (tmmt) REVERT: A 626 LYS cc_start: 0.6464 (OUTLIER) cc_final: 0.4205 (mptp) REVERT: A 633 ILE cc_start: 0.8484 (OUTLIER) cc_final: 0.8239 (mp) REVERT: A 655 SER cc_start: 0.8648 (p) cc_final: 0.8418 (m) REVERT: A 689 MET cc_start: 0.8553 (OUTLIER) cc_final: 0.8342 (mmm) REVERT: A 737 ASP cc_start: 0.8038 (t0) cc_final: 0.7671 (t0) outliers start: 20 outliers final: 10 residues processed: 128 average time/residue: 0.3458 time to fit residues: 45.5646 Evaluate side-chains 135 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 120 time to evaluate : 0.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 296 ARG Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 316 TRP Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 526 LYS Chi-restraints excluded: chain A residue 541 ILE Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 583 GLU Chi-restraints excluded: chain A residue 610 GLU Chi-restraints excluded: chain A residue 626 LYS Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 645 SER Chi-restraints excluded: chain A residue 689 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 24 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 27 optimal weight: 0.8980 chunk 32 optimal weight: 0.9990 chunk 8 optimal weight: 0.6980 chunk 4 optimal weight: 4.9990 chunk 37 optimal weight: 0.9990 chunk 14 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 9 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 513 ASN A 648 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.153432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.136246 restraints weight = 4597.702| |-----------------------------------------------------------------------------| r_work (start): 0.3901 rms_B_bonded: 2.00 r_work: 0.3779 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3623 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.4522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 3094 Z= 0.146 Angle : 0.485 5.729 4190 Z= 0.273 Chirality : 0.042 0.175 506 Planarity : 0.003 0.029 511 Dihedral : 5.415 54.469 411 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 5.08 % Allowed : 26.35 % Favored : 68.57 % 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: 3.05 (0.46), residues: 374 helix: 2.92 (0.33), residues: 233 sheet: 0.73 (0.78), residues: 44 loop : 0.39 (0.76), residues: 97 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 296 TYR 0.028 0.002 TYR A 675 PHE 0.014 0.001 PHE A 344 TRP 0.008 0.001 TRP A 316 HIS 0.005 0.001 HIS A 592 Details of bonding type rmsd covalent geometry : bond 0.00331 ( 3094) covalent geometry : angle 0.48519 ( 4190) hydrogen bonds : bond 0.04628 ( 220) hydrogen bonds : angle 3.85230 ( 654) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 121 time to evaluate : 0.118 Fit side-chains REVERT: A 272 ILE cc_start: 0.8503 (mm) cc_final: 0.8239 (mp) REVERT: A 316 TRP cc_start: 0.8447 (OUTLIER) cc_final: 0.6782 (t60) REVERT: A 535 LEU cc_start: 0.8699 (tm) cc_final: 0.8478 (tp) REVERT: A 581 ILE cc_start: 0.7977 (mm) cc_final: 0.7727 (mp) REVERT: A 582 PHE cc_start: 0.7984 (t80) cc_final: 0.7568 (t80) REVERT: A 610 GLU cc_start: 0.7542 (OUTLIER) cc_final: 0.7324 (mm-30) REVERT: A 624 LYS cc_start: 0.8806 (mmtp) cc_final: 0.6861 (tmmt) REVERT: A 626 LYS cc_start: 0.6467 (OUTLIER) cc_final: 0.4197 (mptp) REVERT: A 633 ILE cc_start: 0.8495 (OUTLIER) cc_final: 0.8232 (mp) REVERT: A 655 SER cc_start: 0.8655 (p) cc_final: 0.8416 (m) REVERT: A 689 MET cc_start: 0.8558 (OUTLIER) cc_final: 0.8346 (mmm) REVERT: A 695 GLU cc_start: 0.7687 (tt0) cc_final: 0.7475 (tt0) REVERT: A 737 ASP cc_start: 0.8015 (t0) cc_final: 0.7644 (t0) outliers start: 16 outliers final: 8 residues processed: 123 average time/residue: 0.4512 time to fit residues: 57.0663 Evaluate side-chains 134 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 121 time to evaluate : 0.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 296 ARG Chi-restraints excluded: chain A residue 316 TRP Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 526 LYS Chi-restraints excluded: chain A residue 541 ILE Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 583 GLU Chi-restraints excluded: chain A residue 610 GLU Chi-restraints excluded: chain A residue 626 LYS Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 645 SER Chi-restraints excluded: chain A residue 689 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 1 optimal weight: 0.9980 chunk 31 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 32 optimal weight: 0.0870 chunk 13 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 chunk 34 optimal weight: 0.0980 chunk 37 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 513 ASN A 648 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.154239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.136847 restraints weight = 4682.946| |-----------------------------------------------------------------------------| r_work (start): 0.3908 rms_B_bonded: 2.05 r_work: 0.3786 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3631 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.4687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 3094 Z= 0.120 Angle : 0.487 6.820 4190 Z= 0.268 Chirality : 0.041 0.173 506 Planarity : 0.003 0.028 511 Dihedral : 5.068 49.488 411 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 4.13 % Allowed : 27.94 % Favored : 67.94 % 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: 3.14 (0.46), residues: 374 helix: 2.99 (0.33), residues: 234 sheet: 0.88 (0.80), residues: 44 loop : 0.35 (0.77), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 296 TYR 0.028 0.002 TYR A 675 PHE 0.017 0.001 PHE A 260 TRP 0.009 0.001 TRP A 304 HIS 0.004 0.001 HIS A 592 Details of bonding type rmsd covalent geometry : bond 0.00261 ( 3094) covalent geometry : angle 0.48715 ( 4190) hydrogen bonds : bond 0.04307 ( 220) hydrogen bonds : angle 3.74554 ( 654) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 122 time to evaluate : 0.109 Fit side-chains revert: symmetry clash REVERT: A 316 TRP cc_start: 0.8443 (OUTLIER) cc_final: 0.6800 (t60) REVERT: A 535 LEU cc_start: 0.8690 (tm) cc_final: 0.8473 (tp) REVERT: A 581 ILE cc_start: 0.7904 (mm) cc_final: 0.7631 (mp) REVERT: A 582 PHE cc_start: 0.8001 (t80) cc_final: 0.7608 (t80) REVERT: A 624 LYS cc_start: 0.8803 (mmtp) cc_final: 0.6861 (tmmt) REVERT: A 626 LYS cc_start: 0.6438 (OUTLIER) cc_final: 0.3872 (mptp) REVERT: A 633 ILE cc_start: 0.8489 (OUTLIER) cc_final: 0.8214 (mp) REVERT: A 655 SER cc_start: 0.8673 (p) cc_final: 0.8402 (m) REVERT: A 689 MET cc_start: 0.8546 (OUTLIER) cc_final: 0.8325 (mmm) REVERT: A 695 GLU cc_start: 0.7676 (tt0) cc_final: 0.7467 (tt0) REVERT: A 737 ASP cc_start: 0.8021 (t0) cc_final: 0.7655 (t0) outliers start: 13 outliers final: 5 residues processed: 125 average time/residue: 0.4180 time to fit residues: 53.6593 Evaluate side-chains 131 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 122 time to evaluate : 0.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 296 ARG Chi-restraints excluded: chain A residue 316 TRP Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 626 LYS Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 645 SER Chi-restraints excluded: chain A residue 689 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 10 optimal weight: 0.7980 chunk 23 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 31 optimal weight: 0.6980 chunk 35 optimal weight: 0.9980 chunk 5 optimal weight: 0.7980 chunk 8 optimal weight: 0.9990 chunk 4 optimal weight: 3.9990 chunk 14 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 513 ASN A 688 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.153697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.136487 restraints weight = 4577.981| |-----------------------------------------------------------------------------| r_work (start): 0.3903 rms_B_bonded: 2.03 r_work: 0.3782 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3628 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.4753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 3094 Z= 0.142 Angle : 0.505 6.876 4190 Z= 0.280 Chirality : 0.043 0.179 506 Planarity : 0.003 0.029 511 Dihedral : 4.886 43.831 411 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 3.17 % Allowed : 29.84 % Favored : 66.98 % 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: 3.05 (0.46), residues: 374 helix: 2.93 (0.33), residues: 234 sheet: 0.81 (0.80), residues: 44 loop : 0.30 (0.77), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 296 TYR 0.029 0.002 TYR A 675 PHE 0.025 0.002 PHE A 330 TRP 0.008 0.001 TRP A 316 HIS 0.005 0.001 HIS A 592 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 3094) covalent geometry : angle 0.50541 ( 4190) hydrogen bonds : bond 0.04522 ( 220) hydrogen bonds : angle 3.84099 ( 654) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 121 time to evaluate : 0.120 Fit side-chains revert: symmetry clash REVERT: A 316 TRP cc_start: 0.8463 (OUTLIER) cc_final: 0.6788 (t60) REVERT: A 535 LEU cc_start: 0.8683 (tm) cc_final: 0.8470 (tp) REVERT: A 582 PHE cc_start: 0.7973 (t80) cc_final: 0.7637 (t80) REVERT: A 624 LYS cc_start: 0.8804 (mmtp) cc_final: 0.6950 (tmmt) REVERT: A 626 LYS cc_start: 0.6455 (OUTLIER) cc_final: 0.3904 (mptp) REVERT: A 633 ILE cc_start: 0.8486 (OUTLIER) cc_final: 0.8221 (mp) REVERT: A 655 SER cc_start: 0.8626 (p) cc_final: 0.8376 (m) REVERT: A 689 MET cc_start: 0.8560 (OUTLIER) cc_final: 0.8349 (mmm) REVERT: A 737 ASP cc_start: 0.8027 (t0) cc_final: 0.7652 (t0) outliers start: 10 outliers final: 6 residues processed: 123 average time/residue: 0.3821 time to fit residues: 48.4685 Evaluate side-chains 131 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 121 time to evaluate : 0.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 296 ARG Chi-restraints excluded: chain A residue 316 TRP Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 583 GLU Chi-restraints excluded: chain A residue 626 LYS Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 645 SER Chi-restraints excluded: chain A residue 689 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 1 optimal weight: 3.9990 chunk 35 optimal weight: 0.9980 chunk 21 optimal weight: 0.9980 chunk 22 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 chunk 16 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 chunk 3 optimal weight: 7.9990 chunk 29 optimal weight: 1.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 688 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.153464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.136330 restraints weight = 4603.643| |-----------------------------------------------------------------------------| r_work (start): 0.3899 rms_B_bonded: 2.03 r_work: 0.3778 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3624 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.4835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3094 Z= 0.150 Angle : 0.506 7.082 4190 Z= 0.279 Chirality : 0.042 0.177 506 Planarity : 0.003 0.029 511 Dihedral : 4.745 38.881 411 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 4.44 % Allowed : 29.21 % Favored : 66.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.99 (0.46), residues: 374 helix: 2.93 (0.33), residues: 234 sheet: 0.74 (0.80), residues: 44 loop : 0.16 (0.77), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 671 TYR 0.027 0.002 TYR A 675 PHE 0.014 0.002 PHE A 260 TRP 0.009 0.001 TRP A 683 HIS 0.004 0.001 HIS A 592 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 3094) covalent geometry : angle 0.50600 ( 4190) hydrogen bonds : bond 0.04474 ( 220) hydrogen bonds : angle 3.81594 ( 654) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1601.09 seconds wall clock time: 27 minutes 52.11 seconds (1672.11 seconds total)