Starting phenix.real_space_refine on Mon Feb 10 21:31:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7v0x_26952/02_2025/7v0x_26952.cif Found real_map, /net/cci-nas-00/data/ceres_data/7v0x_26952/02_2025/7v0x_26952.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7v0x_26952/02_2025/7v0x_26952.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7v0x_26952/02_2025/7v0x_26952.map" model { file = "/net/cci-nas-00/data/ceres_data/7v0x_26952/02_2025/7v0x_26952.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7v0x_26952/02_2025/7v0x_26952.cif" } resolution = 3.0 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= 0.264 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 9 5.16 5 C 1769 2.51 5 N 519 2.21 5 O 521 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 2818 Number of models: 1 Model: "" Number of chains: 1 Chain: "J" Number of atoms: 2818 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 375, 2807 Classifications: {'peptide': 375} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 19, 'TRANS': 355} Chain breaks: 1 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 12 Conformer: "B" Number of residues, atoms: 375, 2807 Classifications: {'peptide': 375} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 19, 'TRANS': 355} Chain breaks: 1 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 12 bond proxies already assigned to first conformer: 2849 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AARG J 591 " occ=0.45 ... (20 atoms not shown) pdb=" NH2BARG J 591 " occ=0.55 Time building chain proxies: 3.77, per 1000 atoms: 1.34 Number of scatterers: 2818 At special positions: 0 Unit cell: (95.45, 85.905, 61.835, 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 9 16.00 O 521 8.00 N 519 7.00 C 1769 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: 0.71 Conformation dependent library (CDL) restraints added in 706.8 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: 698 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 0 sheets defined 61.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'J' and resid 439 through 448 Processing helix chain 'J' and resid 449 through 460 Processing helix chain 'J' and resid 472 through 481 Processing helix chain 'J' and resid 482 through 493 Processing helix chain 'J' and resid 505 through 513 Processing helix chain 'J' and resid 515 through 525 Processing helix chain 'J' and resid 538 through 547 Processing helix chain 'J' and resid 548 through 558 Processing helix chain 'J' and resid 571 through 579 Processing helix chain 'J' and resid 581 through 592 Proline residue: J 590 - end of helix Processing helix chain 'J' and resid 604 through 612 Processing helix chain 'J' and resid 614 through 624 Processing helix chain 'J' and resid 637 through 645 Processing helix chain 'J' and resid 647 through 656 Processing helix chain 'J' and resid 670 through 679 Processing helix chain 'J' and resid 680 through 691 Processing helix chain 'J' and resid 703 through 712 Processing helix chain 'J' and resid 713 through 723 Processing helix chain 'J' and resid 736 through 745 Processing helix chain 'J' and resid 746 through 756 Processing helix chain 'J' and resid 769 through 777 Processing helix chain 'J' and resid 779 through 790 removed outlier: 3.897A pdb=" N VAL J 788 " --> pdb=" O ASP J 784 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N VAL J 789 " --> pdb=" O VAL J 785 " (cutoff:3.500A) 137 hydrogen bonds defined for protein. 411 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: 0.73 Time building geometry restraints manager: 0.84 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: 963 1.34 - 1.46: 496 1.46 - 1.58: 1398 1.58 - 1.69: 0 1.69 - 1.81: 16 Bond restraints: 2873 Sorted by residual: bond pdb=" CA LYS J 460 " pdb=" CB LYS J 460 " ideal model delta sigma weight residual 1.521 1.538 -0.018 1.48e-02 4.57e+03 1.43e+00 bond pdb=" C VAL J 681 " pdb=" N PRO J 682 " ideal model delta sigma weight residual 1.335 1.345 -0.011 1.28e-02 6.10e+03 7.04e-01 bond pdb=" CA LEU J 589 " pdb=" C LEU J 589 " ideal model delta sigma weight residual 1.520 1.531 -0.010 1.23e-02 6.61e+03 6.91e-01 bond pdb=" CA VAL J 681 " pdb=" CB VAL J 681 " ideal model delta sigma weight residual 1.539 1.535 0.004 5.40e-03 3.43e+04 6.36e-01 bond pdb=" C LEU J 589 " pdb=" N PRO J 590 " ideal model delta sigma weight residual 1.335 1.345 -0.010 1.28e-02 6.10e+03 6.33e-01 ... (remaining 2868 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.44: 3767 1.44 - 2.88: 112 2.88 - 4.32: 25 4.32 - 5.76: 4 5.76 - 7.20: 2 Bond angle restraints: 3910 Sorted by residual: angle pdb=" C LYS J 468 " pdb=" N ASP J 469 " pdb=" CA ASP J 469 " ideal model delta sigma weight residual 123.05 126.53 -3.48 1.57e+00 4.06e-01 4.91e+00 angle pdb=" C LYS J 525 " pdb=" N GLU J 526 " pdb=" CA GLU J 526 " ideal model delta sigma weight residual 122.35 125.42 -3.07 1.46e+00 4.69e-01 4.43e+00 angle pdb=" C GLN J 458 " pdb=" N ASN J 459 " pdb=" CA ASN J 459 " ideal model delta sigma weight residual 120.89 117.77 3.12 1.50e+00 4.44e-01 4.32e+00 angle pdb=" CA LEU J 777 " pdb=" CB LEU J 777 " pdb=" CG LEU J 777 " ideal model delta sigma weight residual 116.30 123.50 -7.20 3.50e+00 8.16e-02 4.23e+00 angle pdb=" C HIS J 723 " pdb=" N GLN J 724 " pdb=" CA GLN J 724 " ideal model delta sigma weight residual 122.35 125.33 -2.98 1.46e+00 4.69e-01 4.17e+00 ... (remaining 3905 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.15: 1459 17.15 - 34.31: 177 34.31 - 51.46: 81 51.46 - 68.61: 20 68.61 - 85.76: 4 Dihedral angle restraints: 1741 sinusoidal: 660 harmonic: 1081 Sorted by residual: dihedral pdb=" CA ARG J 558 " pdb=" C ARG J 558 " pdb=" N ASP J 559 " pdb=" CA ASP J 559 " ideal model delta harmonic sigma weight residual 180.00 162.01 17.99 0 5.00e+00 4.00e-02 1.29e+01 dihedral pdb=" CA ASP J 470 " pdb=" CB ASP J 470 " pdb=" CG ASP J 470 " pdb=" OD1 ASP J 470 " ideal model delta sinusoidal sigma weight residual -30.00 -83.79 53.79 1 2.00e+01 2.50e-03 9.82e+00 dihedral pdb=" CA LEU J 587 " pdb=" CB LEU J 587 " pdb=" CG LEU J 587 " pdb=" CD1 LEU J 587 " ideal model delta sinusoidal sigma weight residual 60.00 118.08 -58.08 3 1.50e+01 4.44e-03 9.46e+00 ... (remaining 1738 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 306 0.027 - 0.055: 81 0.055 - 0.082: 47 0.082 - 0.109: 29 0.109 - 0.137: 2 Chirality restraints: 465 Sorted by residual: chirality pdb=" CA ILE J 813 " pdb=" N ILE J 813 " pdb=" C ILE J 813 " pdb=" CB ILE J 813 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.68e-01 chirality pdb=" CA LEU J 777 " pdb=" N LEU J 777 " pdb=" C LEU J 777 " pdb=" CB LEU J 777 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.49e-01 chirality pdb=" CA GLU J 526 " pdb=" N GLU J 526 " pdb=" C GLU J 526 " pdb=" CB GLU J 526 " both_signs ideal model delta sigma weight residual False 2.51 2.40 0.11 2.00e-01 2.50e+01 2.95e-01 ... (remaining 462 not shown) Planarity restraints: 507 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR J 439 " 0.026 5.00e-02 4.00e+02 4.01e-02 2.57e+00 pdb=" N PRO J 440 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO J 440 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO J 440 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR J 670 " 0.025 5.00e-02 4.00e+02 3.82e-02 2.34e+00 pdb=" N PRO J 671 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO J 671 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO J 671 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR J 637 " 0.025 5.00e-02 4.00e+02 3.81e-02 2.32e+00 pdb=" N PRO J 638 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO J 638 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO J 638 " 0.021 5.00e-02 4.00e+02 ... (remaining 504 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 310 2.75 - 3.29: 2680 3.29 - 3.82: 5094 3.82 - 4.36: 5974 4.36 - 4.90: 9758 Nonbonded interactions: 23816 Sorted by model distance: nonbonded pdb=" O LEU J 786 " pdb=" OG1 THR J 790 " model vdw 2.211 3.040 nonbonded pdb=" N ASN J 484 " pdb=" OD1 ASN J 484 " model vdw 2.299 3.120 nonbonded pdb=" NE2 GLN J 529 " pdb=" O ARG J 558 " model vdw 2.325 3.120 nonbonded pdb=" O ALA J 676 " pdb=" ND2 ASN J 713 " model vdw 2.392 3.120 nonbonded pdb=" OG1 THR J 439 " pdb=" ND1 HIS J 442 " model vdw 2.423 3.120 ... (remaining 23811 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=0.45 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: 0.010 Normalize map: mean=0, sd=1: 1.090 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: 0.260 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 13.750 Find NCS groups from input model: 0.030 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:12.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 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 : 0.002 0.027 2873 Z= 0.152 Angle : 0.628 7.197 3910 Z= 0.347 Chirality : 0.038 0.137 465 Planarity : 0.005 0.040 507 Dihedral : 19.061 85.765 1043 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 5.05 % Allowed : 24.58 % Favored : 70.37 % 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: 0.72 (0.41), residues: 374 helix: 0.63 (0.32), residues: 234 sheet: None (None), residues: 0 loop : 0.48 (0.49), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP J 600 HIS 0.004 0.001 HIS J 515 PHE 0.006 0.001 PHE J 719 TYR 0.013 0.001 TYR J 546 ARG 0.002 0.000 ARG J 446 *********************** 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 69 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 55 time to evaluate : 0.280 Fit side-chains outliers start: 14 outliers final: 13 residues processed: 69 average time/residue: 1.0463 time to fit residues: 74.3053 Evaluate side-chains 65 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 52 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 437 VAL Chi-restraints excluded: chain J residue 459 ASN Chi-restraints excluded: chain J residue 460 LYS Chi-restraints excluded: chain J residue 472 THR Chi-restraints excluded: chain J residue 484 ASN Chi-restraints excluded: chain J residue 509 ILE Chi-restraints excluded: chain J residue 667 SER Chi-restraints excluded: chain J residue 688 ILE Chi-restraints excluded: chain J residue 716 LEU Chi-restraints excluded: chain J residue 730 LYS Chi-restraints excluded: chain J residue 736 SER Chi-restraints excluded: chain J residue 747 THR Chi-restraints excluded: chain J residue 788 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 31 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 9 optimal weight: 8.9990 chunk 18 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 29 optimal weight: 0.0570 chunk 11 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 overall best weight: 1.1904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 578 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.138889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.109326 restraints weight = 11472.962| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 3.05 r_work: 0.2839 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2803 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2803 r_free = 0.2803 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2803 r_free = 0.2803 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2803 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.0948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 2873 Z= 0.168 Angle : 0.524 5.149 3910 Z= 0.264 Chirality : 0.039 0.141 465 Planarity : 0.005 0.032 507 Dihedral : 8.770 50.839 418 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 4.71 % Allowed : 25.59 % Favored : 69.70 % 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: 1.38 (0.42), residues: 374 helix: 1.13 (0.33), residues: 235 sheet: None (None), residues: 0 loop : 0.77 (0.51), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.001 TRP J 600 HIS 0.004 0.001 HIS J 449 PHE 0.006 0.001 PHE J 719 TYR 0.009 0.001 TYR J 546 ARG 0.002 0.000 ARG J 446 *********************** 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 68 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 55 time to evaluate : 0.321 Fit side-chains REVERT: J 484 ASN cc_start: 0.6484 (OUTLIER) cc_final: 0.6165 (p0) REVERT: J 692 VAL cc_start: 0.8551 (t) cc_final: 0.8306 (m) REVERT: J 700 MET cc_start: 0.8082 (OUTLIER) cc_final: 0.7442 (mtm) outliers start: 13 outliers final: 5 residues processed: 64 average time/residue: 0.9876 time to fit residues: 65.2078 Evaluate side-chains 59 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 52 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 484 ASN Chi-restraints excluded: chain J residue 501 THR Chi-restraints excluded: chain J residue 688 ILE Chi-restraints excluded: chain J residue 700 MET Chi-restraints excluded: chain J residue 716 LEU Chi-restraints excluded: chain J residue 730 LYS Chi-restraints excluded: chain J residue 747 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 19 optimal weight: 4.9990 chunk 11 optimal weight: 0.8980 chunk 25 optimal weight: 0.9980 chunk 20 optimal weight: 3.9990 chunk 33 optimal weight: 6.9990 chunk 8 optimal weight: 7.9990 chunk 5 optimal weight: 0.6980 chunk 14 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 492 ASN ** 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 = 0.3423 r_free = 0.3423 target = 0.138795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.108060 restraints weight = 10657.127| |-----------------------------------------------------------------------------| r_work (start): 0.3042 rms_B_bonded: 3.04 r_work: 0.2800 rms_B_bonded: 4.92 restraints_weight: 0.5000 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2771 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2771 r_free = 0.2771 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2771 r_free = 0.2771 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2771 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.1151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 2873 Z= 0.155 Angle : 0.507 5.488 3910 Z= 0.253 Chirality : 0.038 0.128 465 Planarity : 0.005 0.032 507 Dihedral : 6.542 51.295 405 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 3.70 % Allowed : 25.25 % Favored : 71.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.66 (0.43), residues: 374 helix: 1.38 (0.33), residues: 235 sheet: None (None), residues: 0 loop : 0.84 (0.52), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP J 600 HIS 0.004 0.001 HIS J 723 PHE 0.005 0.001 PHE J 719 TYR 0.009 0.001 TYR J 546 ARG 0.002 0.000 ARG J 446 *********************** 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 63 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 53 time to evaluate : 0.289 Fit side-chains REVERT: J 550 ARG cc_start: 0.7936 (OUTLIER) cc_final: 0.7588 (mmt90) REVERT: J 692 VAL cc_start: 0.8519 (t) cc_final: 0.8209 (m) REVERT: J 700 MET cc_start: 0.8115 (OUTLIER) cc_final: 0.7468 (mtm) outliers start: 10 outliers final: 4 residues processed: 58 average time/residue: 1.0326 time to fit residues: 61.8861 Evaluate side-chains 59 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 53 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 501 THR Chi-restraints excluded: chain J residue 526 GLU Chi-restraints excluded: chain J residue 550 ARG Chi-restraints excluded: chain J residue 688 ILE Chi-restraints excluded: chain J residue 700 MET Chi-restraints excluded: chain J residue 716 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 7 optimal weight: 0.7980 chunk 22 optimal weight: 6.9990 chunk 32 optimal weight: 6.9990 chunk 30 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 9 optimal weight: 9.9990 chunk 34 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 492 ASN ** 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 = 0.3431 r_free = 0.3431 target = 0.139370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.108728 restraints weight = 9425.541| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 3.11 r_work: 0.2848 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2825 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2825 r_free = 0.2825 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2825 r_free = 0.2825 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2825 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.1272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 2873 Z= 0.137 Angle : 0.489 4.957 3910 Z= 0.242 Chirality : 0.038 0.129 465 Planarity : 0.004 0.032 507 Dihedral : 5.451 43.021 398 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 3.70 % Allowed : 25.59 % Favored : 70.71 % 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: 1.83 (0.43), residues: 374 helix: 1.53 (0.34), residues: 235 sheet: None (None), residues: 0 loop : 0.88 (0.52), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP J 600 HIS 0.004 0.001 HIS J 723 PHE 0.004 0.001 PHE J 719 TYR 0.008 0.001 TYR J 546 ARG 0.002 0.000 ARG J 446 *********************** 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 66 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 56 time to evaluate : 0.294 Fit side-chains REVERT: J 550 ARG cc_start: 0.7860 (OUTLIER) cc_final: 0.7584 (mmt90) REVERT: J 692 VAL cc_start: 0.8409 (t) cc_final: 0.8088 (m) REVERT: J 700 MET cc_start: 0.7985 (OUTLIER) cc_final: 0.7386 (mtm) outliers start: 10 outliers final: 6 residues processed: 60 average time/residue: 0.9550 time to fit residues: 59.4373 Evaluate side-chains 62 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 54 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 501 THR Chi-restraints excluded: chain J residue 516 VAL Chi-restraints excluded: chain J residue 526 GLU Chi-restraints excluded: chain J residue 550 ARG Chi-restraints excluded: chain J residue 688 ILE Chi-restraints excluded: chain J residue 700 MET Chi-restraints excluded: chain J residue 716 LEU Chi-restraints excluded: chain J residue 736 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 17 optimal weight: 5.9990 chunk 34 optimal weight: 6.9990 chunk 7 optimal weight: 3.9990 chunk 27 optimal weight: 6.9990 chunk 3 optimal weight: 0.2980 chunk 18 optimal weight: 0.7980 chunk 19 optimal weight: 5.9990 chunk 21 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 9 optimal weight: 5.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 492 ASN ** 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 = 0.3385 r_free = 0.3385 target = 0.135320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.106381 restraints weight = 6310.932| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 2.25 r_work: 0.2828 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2808 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2808 r_free = 0.2808 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2808 r_free = 0.2808 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2808 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.1431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 2873 Z= 0.245 Angle : 0.540 5.356 3910 Z= 0.272 Chirality : 0.041 0.135 465 Planarity : 0.005 0.034 507 Dihedral : 5.755 48.494 398 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 4.71 % Allowed : 24.92 % Favored : 70.37 % 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: 1.64 (0.43), residues: 374 helix: 1.34 (0.33), residues: 235 sheet: None (None), residues: 0 loop : 0.88 (0.54), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP J 600 HIS 0.005 0.001 HIS J 723 PHE 0.005 0.002 PHE J 719 TYR 0.010 0.002 TYR J 735 ARG 0.002 0.000 ARG J 446 *********************** 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 62 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 50 time to evaluate : 0.325 Fit side-chains REVERT: J 550 ARG cc_start: 0.7902 (OUTLIER) cc_final: 0.7519 (mmt90) REVERT: J 700 MET cc_start: 0.8094 (OUTLIER) cc_final: 0.7458 (mtm) outliers start: 12 outliers final: 7 residues processed: 55 average time/residue: 1.0408 time to fit residues: 59.0215 Evaluate side-chains 56 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 47 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 501 THR Chi-restraints excluded: chain J residue 516 VAL Chi-restraints excluded: chain J residue 526 GLU Chi-restraints excluded: chain J residue 550 ARG Chi-restraints excluded: chain J residue 587 LEU Chi-restraints excluded: chain J residue 688 ILE Chi-restraints excluded: chain J residue 700 MET Chi-restraints excluded: chain J residue 716 LEU Chi-restraints excluded: chain J residue 736 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 12 optimal weight: 4.9990 chunk 33 optimal weight: 4.9990 chunk 2 optimal weight: 9.9990 chunk 8 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 14 optimal weight: 0.9980 chunk 10 optimal weight: 4.9990 chunk 15 optimal weight: 0.0970 chunk 24 optimal weight: 0.8980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 492 ASN ** 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 = 0.3408 r_free = 0.3408 target = 0.137497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.107142 restraints weight = 8408.436| |-----------------------------------------------------------------------------| r_work (start): 0.3026 rms_B_bonded: 2.63 r_work: 0.2829 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2805 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2805 r_free = 0.2805 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2805 r_free = 0.2805 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2805 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.1416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 2873 Z= 0.150 Angle : 0.493 5.469 3910 Z= 0.246 Chirality : 0.038 0.129 465 Planarity : 0.005 0.033 507 Dihedral : 5.736 55.019 398 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 3.37 % Allowed : 26.26 % Favored : 70.37 % 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: 1.85 (0.43), residues: 374 helix: 1.52 (0.34), residues: 235 sheet: None (None), residues: 0 loop : 0.94 (0.54), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.001 TRP J 600 HIS 0.004 0.001 HIS J 723 PHE 0.004 0.001 PHE J 719 TYR 0.008 0.001 TYR J 546 ARG 0.002 0.000 ARG J 446 *********************** 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 59 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 51 time to evaluate : 0.291 Fit side-chains REVERT: J 550 ARG cc_start: 0.7880 (OUTLIER) cc_final: 0.7603 (mmt90) REVERT: J 700 MET cc_start: 0.8032 (OUTLIER) cc_final: 0.7432 (mtm) outliers start: 8 outliers final: 6 residues processed: 55 average time/residue: 1.0110 time to fit residues: 57.3984 Evaluate side-chains 59 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 51 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 516 VAL Chi-restraints excluded: chain J residue 526 GLU Chi-restraints excluded: chain J residue 550 ARG Chi-restraints excluded: chain J residue 587 LEU Chi-restraints excluded: chain J residue 688 ILE Chi-restraints excluded: chain J residue 700 MET Chi-restraints excluded: chain J residue 716 LEU Chi-restraints excluded: chain J residue 736 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 30 optimal weight: 3.9990 chunk 19 optimal weight: 7.9990 chunk 7 optimal weight: 0.8980 chunk 12 optimal weight: 4.9990 chunk 34 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 2 optimal weight: 9.9990 chunk 1 optimal weight: 6.9990 chunk 16 optimal weight: 0.7980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 442 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 492 ASN ** 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 = 0.3401 r_free = 0.3401 target = 0.136608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.107652 restraints weight = 6764.865| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 2.31 r_work: 0.2850 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2828 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2828 r_free = 0.2828 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2827 r_free = 0.2827 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2827 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.1473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 2873 Z= 0.173 Angle : 0.501 5.691 3910 Z= 0.250 Chirality : 0.039 0.131 465 Planarity : 0.005 0.033 507 Dihedral : 5.822 57.617 398 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 4.38 % Allowed : 25.25 % Favored : 70.37 % 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: 1.81 (0.43), residues: 374 helix: 1.48 (0.33), residues: 235 sheet: None (None), residues: 0 loop : 0.94 (0.55), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.001 TRP J 600 HIS 0.005 0.001 HIS J 723 PHE 0.004 0.001 PHE J 719 TYR 0.009 0.001 TYR J 546 ARG 0.001 0.000 ARG J 803 *********************** 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 61 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 50 time to evaluate : 0.320 Fit side-chains REVERT: J 550 ARG cc_start: 0.7886 (OUTLIER) cc_final: 0.7602 (mmt90) REVERT: J 700 MET cc_start: 0.8019 (OUTLIER) cc_final: 0.7419 (mtm) outliers start: 11 outliers final: 6 residues processed: 55 average time/residue: 1.0821 time to fit residues: 61.3780 Evaluate side-chains 58 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 50 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 501 THR Chi-restraints excluded: chain J residue 516 VAL Chi-restraints excluded: chain J residue 526 GLU Chi-restraints excluded: chain J residue 550 ARG Chi-restraints excluded: chain J residue 587 LEU Chi-restraints excluded: chain J residue 688 ILE Chi-restraints excluded: chain J residue 700 MET Chi-restraints excluded: chain J residue 736 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 7 optimal weight: 0.9990 chunk 33 optimal weight: 5.9990 chunk 6 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 27 optimal weight: 6.9990 chunk 2 optimal weight: 10.0000 chunk 11 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 chunk 34 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 442 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 492 ASN ** 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 = 0.3403 r_free = 0.3403 target = 0.136867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.106053 restraints weight = 10554.296| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 3.09 r_work: 0.2811 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2788 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2788 r_free = 0.2788 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2788 r_free = 0.2788 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2788 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.1465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 2873 Z= 0.169 Angle : 0.504 6.665 3910 Z= 0.250 Chirality : 0.038 0.131 465 Planarity : 0.005 0.033 507 Dihedral : 4.702 37.887 396 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 4.38 % Allowed : 25.25 % Favored : 70.37 % 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: 1.84 (0.43), residues: 374 helix: 1.51 (0.34), residues: 235 sheet: None (None), residues: 0 loop : 0.95 (0.55), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.001 TRP J 600 HIS 0.004 0.001 HIS J 723 PHE 0.004 0.001 PHE J 719 TYR 0.009 0.001 TYR J 546 ARG 0.001 0.000 ARG J 803 *********************** 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 61 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 50 time to evaluate : 0.291 Fit side-chains REVERT: J 550 ARG cc_start: 0.7873 (OUTLIER) cc_final: 0.7600 (mmt90) REVERT: J 700 MET cc_start: 0.8054 (OUTLIER) cc_final: 0.7426 (mtm) outliers start: 11 outliers final: 7 residues processed: 56 average time/residue: 1.1061 time to fit residues: 63.7272 Evaluate side-chains 59 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 50 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 501 THR Chi-restraints excluded: chain J residue 516 VAL Chi-restraints excluded: chain J residue 526 GLU Chi-restraints excluded: chain J residue 550 ARG Chi-restraints excluded: chain J residue 587 LEU Chi-restraints excluded: chain J residue 688 ILE Chi-restraints excluded: chain J residue 700 MET Chi-restraints excluded: chain J residue 716 LEU Chi-restraints excluded: chain J residue 736 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 6 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 2 optimal weight: 8.9990 chunk 1 optimal weight: 6.9990 chunk 8 optimal weight: 3.9990 chunk 18 optimal weight: 4.9990 chunk 35 optimal weight: 7.9990 chunk 29 optimal weight: 6.9990 chunk 34 optimal weight: 0.9980 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 442 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 492 ASN ** 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 = 0.3400 r_free = 0.3400 target = 0.136599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.107362 restraints weight = 7215.011| |-----------------------------------------------------------------------------| r_work (start): 0.3028 rms_B_bonded: 2.39 r_work: 0.2839 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2819 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2819 r_free = 0.2819 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2819 r_free = 0.2819 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2819 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.1511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2873 Z= 0.180 Angle : 0.508 6.019 3910 Z= 0.253 Chirality : 0.039 0.132 465 Planarity : 0.005 0.034 507 Dihedral : 4.728 37.965 396 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 3.70 % Allowed : 25.93 % Favored : 70.37 % 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: 1.79 (0.43), residues: 374 helix: 1.47 (0.34), residues: 235 sheet: None (None), residues: 0 loop : 0.93 (0.55), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP J 600 HIS 0.005 0.001 HIS J 723 PHE 0.004 0.001 PHE J 719 TYR 0.009 0.001 TYR J 546 ARG 0.002 0.000 ARG J 803 *********************** 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 60 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 51 time to evaluate : 0.298 Fit side-chains REVERT: J 550 ARG cc_start: 0.7888 (OUTLIER) cc_final: 0.7604 (mmt90) REVERT: J 700 MET cc_start: 0.8032 (OUTLIER) cc_final: 0.7430 (mtm) outliers start: 9 outliers final: 6 residues processed: 55 average time/residue: 1.1160 time to fit residues: 63.1605 Evaluate side-chains 59 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 51 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 501 THR Chi-restraints excluded: chain J residue 516 VAL Chi-restraints excluded: chain J residue 526 GLU Chi-restraints excluded: chain J residue 550 ARG Chi-restraints excluded: chain J residue 587 LEU Chi-restraints excluded: chain J residue 688 ILE Chi-restraints excluded: chain J residue 700 MET Chi-restraints excluded: chain J residue 736 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 17 optimal weight: 0.0270 chunk 29 optimal weight: 5.9990 chunk 32 optimal weight: 0.8980 chunk 28 optimal weight: 0.8980 chunk 8 optimal weight: 6.9990 chunk 21 optimal weight: 1.9990 chunk 9 optimal weight: 8.9990 chunk 10 optimal weight: 0.6980 chunk 2 optimal weight: 10.0000 chunk 27 optimal weight: 4.9990 chunk 11 optimal weight: 0.7980 overall best weight: 0.6638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 442 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 = 0.3428 r_free = 0.3428 target = 0.138984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.110017 restraints weight = 7358.448| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 2.39 r_work: 0.2880 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2857 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2857 r_free = 0.2857 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2857 r_free = 0.2857 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2857 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.1513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 2873 Z= 0.136 Angle : 0.482 6.103 3910 Z= 0.238 Chirality : 0.037 0.125 465 Planarity : 0.005 0.033 507 Dihedral : 4.565 36.300 396 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 3.03 % Allowed : 26.60 % Favored : 70.37 % 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: 1.99 (0.44), residues: 374 helix: 1.63 (0.34), residues: 235 sheet: None (None), residues: 0 loop : 0.98 (0.55), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP J 600 HIS 0.004 0.001 HIS J 723 PHE 0.004 0.001 PHE J 719 TYR 0.008 0.001 TYR J 546 ARG 0.002 0.000 ARG J 803 ********************** 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 59 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 52 time to evaluate : 0.296 Fit side-chains REVERT: J 471 GLN cc_start: 0.8035 (OUTLIER) cc_final: 0.7752 (mt0) REVERT: J 550 ARG cc_start: 0.7881 (OUTLIER) cc_final: 0.7601 (mmt90) REVERT: J 700 MET cc_start: 0.7926 (mtp) cc_final: 0.7389 (mtm) outliers start: 7 outliers final: 3 residues processed: 54 average time/residue: 1.0411 time to fit residues: 57.9358 Evaluate side-chains 54 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 49 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 471 GLN Chi-restraints excluded: chain J residue 516 VAL Chi-restraints excluded: chain J residue 526 GLU Chi-restraints excluded: chain J residue 550 ARG Chi-restraints excluded: chain J residue 736 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 9 optimal weight: 7.9990 chunk 16 optimal weight: 0.4980 chunk 35 optimal weight: 0.0670 chunk 14 optimal weight: 0.0370 chunk 4 optimal weight: 9.9990 chunk 22 optimal weight: 6.9990 chunk 3 optimal weight: 4.9990 chunk 29 optimal weight: 0.0010 chunk 31 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 7 optimal weight: 0.7980 overall best weight: 0.2802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 442 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 = 0.3463 r_free = 0.3463 target = 0.141979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.111606 restraints weight = 9492.395| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 2.74 r_work: 0.2881 rms_B_bonded: 4.57 restraints_weight: 0.5000 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2858 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2858 r_free = 0.2858 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2858 r_free = 0.2858 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2858 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.1613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 2873 Z= 0.115 Angle : 0.470 6.024 3910 Z= 0.233 Chirality : 0.037 0.123 465 Planarity : 0.005 0.033 507 Dihedral : 4.047 17.312 394 Min Nonbonded Distance : 2.643 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 2.69 % Allowed : 26.94 % Favored : 70.37 % 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: 2.13 (0.44), residues: 374 helix: 1.78 (0.34), residues: 235 sheet: None (None), residues: 0 loop : 0.99 (0.55), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP J 600 HIS 0.004 0.001 HIS J 442 PHE 0.004 0.001 PHE J 719 TYR 0.008 0.001 TYR J 546 ARG 0.002 0.000 ARG J 803 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3029.72 seconds wall clock time: 53 minutes 57.79 seconds (3237.79 seconds total)