Starting phenix.real_space_refine on Wed Sep 17 06:28:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9f0l_50113/09_2025/9f0l_50113_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9f0l_50113/09_2025/9f0l_50113.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9f0l_50113/09_2025/9f0l_50113_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9f0l_50113/09_2025/9f0l_50113_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9f0l_50113/09_2025/9f0l_50113.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9f0l_50113/09_2025/9f0l_50113.map" } resolution = 2.76 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= 0.012 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: 3 Type Number sf(0) Gaussians C 3952 2.51 5 N 1064 2.21 5 O 1103 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6119 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 6119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 791, 6119 Classifications: {'peptide': 791} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'PTRANS': 33, 'TRANS': 757} Chain breaks: 1 Unresolved non-hydrogen bonds: 161 Unresolved non-hydrogen angles: 205 Unresolved non-hydrogen dihedrals: 131 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 8, 'GLU:plan': 19, 'TRP:plan': 1, 'HIS:plan': 1, 'TYR:plan': 1, 'PHE:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 130 Time building chain proxies: 1.60, per 1000 atoms: 0.26 Number of scatterers: 6119 At special positions: 0 Unit cell: (88.92, 78.66, 112.86, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 1103 8.00 N 1064 7.00 C 3952 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: 0.53 Conformation dependent library (CDL) restraints added in 298.3 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1524 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 1 sheets defined 83.7% alpha, 2.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.14 Creating SS restraints... Processing helix chain 'A' and resid 147 through 169 removed outlier: 3.529A pdb=" N VAL A 153 " --> pdb=" O ALA A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 191 removed outlier: 3.807A pdb=" N GLU A 191 " --> pdb=" O GLU A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 221 Processing helix chain 'A' and resid 224 through 240 Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 260 through 282 Processing helix chain 'A' and resid 284 through 295 Processing helix chain 'A' and resid 298 through 300 No H-bonds generated for 'chain 'A' and resid 298 through 300' Processing helix chain 'A' and resid 301 through 329 Processing helix chain 'A' and resid 333 through 353 Processing helix chain 'A' and resid 355 through 372 Processing helix chain 'A' and resid 374 through 408 Processing helix chain 'A' and resid 409 through 429 removed outlier: 3.558A pdb=" N LYS A 413 " --> pdb=" O ASP A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 439 Processing helix chain 'A' and resid 440 through 459 Processing helix chain 'A' and resid 473 through 492 Processing helix chain 'A' and resid 494 through 510 removed outlier: 3.814A pdb=" N ALA A 498 " --> pdb=" O ASP A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 524 Processing helix chain 'A' and resid 527 through 549 removed outlier: 3.791A pdb=" N LEU A 531 " --> pdb=" O SER A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 586 removed outlier: 3.667A pdb=" N LEU A 560 " --> pdb=" O ASP A 556 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N GLU A 567 " --> pdb=" O GLU A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 593 through 620 removed outlier: 3.862A pdb=" N ILE A 620 " --> pdb=" O GLU A 616 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 624 Processing helix chain 'A' and resid 625 through 644 Processing helix chain 'A' and resid 648 through 663 removed outlier: 3.555A pdb=" N PHE A 655 " --> pdb=" O GLU A 651 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N SER A 656 " --> pdb=" O LEU A 652 " (cutoff:3.500A) Processing helix chain 'A' and resid 669 through 686 Processing helix chain 'A' and resid 688 through 704 removed outlier: 3.788A pdb=" N VAL A 692 " --> pdb=" O ALA A 688 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ARG A 698 " --> pdb=" O GLU A 694 " (cutoff:3.500A) Processing helix chain 'A' and resid 709 through 731 removed outlier: 3.591A pdb=" N LEU A 715 " --> pdb=" O GLU A 711 " (cutoff:3.500A) Processing helix chain 'A' and resid 732 through 741 Processing helix chain 'A' and resid 743 through 747 removed outlier: 3.883A pdb=" N ILE A 747 " --> pdb=" O PRO A 744 " (cutoff:3.500A) Processing helix chain 'A' and resid 779 through 811 Processing helix chain 'A' and resid 817 through 850 Processing helix chain 'A' and resid 856 through 875 Processing helix chain 'A' and resid 879 through 885 Processing helix chain 'A' and resid 886 through 901 Processing helix chain 'A' and resid 906 through 922 removed outlier: 3.617A pdb=" N GLU A 911 " --> pdb=" O PRO A 907 " (cutoff:3.500A) Processing helix chain 'A' and resid 924 through 940 Processing sheet with id=AA1, first strand: chain 'A' and resid 463 through 468 520 hydrogen bonds defined for protein. 1545 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.02 Time building geometry restraints manager: 0.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.29: 1038 1.29 - 1.36: 1039 1.36 - 1.42: 435 1.42 - 1.49: 926 1.49 - 1.55: 2783 Bond restraints: 6221 Sorted by residual: bond pdb=" CB GLU A 616 " pdb=" CG GLU A 616 " ideal model delta sigma weight residual 1.520 1.550 -0.030 3.00e-02 1.11e+03 1.02e+00 bond pdb=" CG1 ILE A 658 " pdb=" CD1 ILE A 658 " ideal model delta sigma weight residual 1.513 1.476 0.037 3.90e-02 6.57e+02 9.05e-01 bond pdb=" CA GLU A 616 " pdb=" CB GLU A 616 " ideal model delta sigma weight residual 1.529 1.542 -0.013 1.78e-02 3.16e+03 5.42e-01 bond pdb=" CG LYS A 762 " pdb=" CD LYS A 762 " ideal model delta sigma weight residual 1.520 1.500 0.020 3.00e-02 1.11e+03 4.53e-01 bond pdb=" N GLU A 616 " pdb=" CA GLU A 616 " ideal model delta sigma weight residual 1.457 1.466 -0.009 1.35e-02 5.49e+03 4.40e-01 ... (remaining 6216 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.23: 8307 1.23 - 2.47: 95 2.47 - 3.70: 34 3.70 - 4.93: 6 4.93 - 6.16: 6 Bond angle restraints: 8448 Sorted by residual: angle pdb=" C ILE A 615 " pdb=" N GLU A 616 " pdb=" CA GLU A 616 " ideal model delta sigma weight residual 121.18 115.65 5.53 1.98e+00 2.55e-01 7.80e+00 angle pdb=" CB GLU A 616 " pdb=" CG GLU A 616 " pdb=" CD GLU A 616 " ideal model delta sigma weight residual 112.60 116.71 -4.11 1.70e+00 3.46e-01 5.83e+00 angle pdb=" CA GLU A 616 " pdb=" CB GLU A 616 " pdb=" CG GLU A 616 " ideal model delta sigma weight residual 114.10 118.88 -4.78 2.00e+00 2.50e-01 5.71e+00 angle pdb=" N GLU A 616 " pdb=" CA GLU A 616 " pdb=" CB GLU A 616 " ideal model delta sigma weight residual 110.39 114.52 -4.13 1.75e+00 3.27e-01 5.57e+00 angle pdb=" N GLY A 776 " pdb=" CA GLY A 776 " pdb=" C GLY A 776 " ideal model delta sigma weight residual 113.18 118.08 -4.90 2.37e+00 1.78e-01 4.27e+00 ... (remaining 8443 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.67: 3232 17.67 - 35.34: 407 35.34 - 53.00: 133 53.00 - 70.67: 32 70.67 - 88.34: 11 Dihedral angle restraints: 3815 sinusoidal: 1484 harmonic: 2331 Sorted by residual: dihedral pdb=" CG ARG A 784 " pdb=" CD ARG A 784 " pdb=" NE ARG A 784 " pdb=" CZ ARG A 784 " ideal model delta sinusoidal sigma weight residual 180.00 135.04 44.96 2 1.50e+01 4.44e-03 1.07e+01 dihedral pdb=" CA GLU A 867 " pdb=" C GLU A 867 " pdb=" N SER A 868 " pdb=" CA SER A 868 " ideal model delta harmonic sigma weight residual 180.00 163.73 16.27 0 5.00e+00 4.00e-02 1.06e+01 dihedral pdb=" CG ARG A 690 " pdb=" CD ARG A 690 " pdb=" NE ARG A 690 " pdb=" CZ ARG A 690 " ideal model delta sinusoidal sigma weight residual 90.00 134.64 -44.64 2 1.50e+01 4.44e-03 1.05e+01 ... (remaining 3812 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 791 0.037 - 0.074: 162 0.074 - 0.111: 41 0.111 - 0.148: 8 0.148 - 0.185: 3 Chirality restraints: 1005 Sorted by residual: chirality pdb=" CA GLU A 616 " pdb=" N GLU A 616 " pdb=" C GLU A 616 " pdb=" CB GLU A 616 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.54e-01 chirality pdb=" CA GLU A 867 " pdb=" N GLU A 867 " pdb=" C GLU A 867 " pdb=" CB GLU A 867 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 6.91e-01 chirality pdb=" CB ILE A 636 " pdb=" CA ILE A 636 " pdb=" CG1 ILE A 636 " pdb=" CG2 ILE A 636 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.15 2.00e-01 2.50e+01 5.94e-01 ... (remaining 1002 not shown) Planarity restraints: 1094 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU A 867 " 0.008 2.00e-02 2.50e+03 1.58e-02 2.51e+00 pdb=" C GLU A 867 " -0.027 2.00e-02 2.50e+03 pdb=" O GLU A 867 " 0.010 2.00e-02 2.50e+03 pdb=" N SER A 868 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 779 " 0.026 5.00e-02 4.00e+02 3.90e-02 2.43e+00 pdb=" N PRO A 780 " -0.067 5.00e-02 4.00e+02 pdb=" CA PRO A 780 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 780 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 185 " 0.024 5.00e-02 4.00e+02 3.59e-02 2.06e+00 pdb=" N PRO A 186 " -0.062 5.00e-02 4.00e+02 pdb=" CA PRO A 186 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 186 " 0.020 5.00e-02 4.00e+02 ... (remaining 1091 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 1424 2.80 - 3.32: 6073 3.32 - 3.85: 10636 3.85 - 4.37: 11927 4.37 - 4.90: 21156 Nonbonded interactions: 51216 Sorted by model distance: nonbonded pdb=" OH TYR A 491 " pdb=" OD1 ASP A 536 " model vdw 2.271 3.040 nonbonded pdb=" O ILE A 332 " pdb=" NE2 GLN A 337 " model vdw 2.307 3.120 nonbonded pdb=" OD1 ASP A 425 " pdb=" NH2 ARG A 778 " model vdw 2.340 3.120 nonbonded pdb=" O LEU A 426 " pdb=" OG1 THR A 432 " model vdw 2.365 3.040 nonbonded pdb=" NE2 GLN A 545 " pdb=" OD1 ASP A 553 " model vdw 2.393 3.120 ... (remaining 51211 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 7.300 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 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 0.037 6221 Z= 0.101 Angle : 0.433 6.163 8448 Z= 0.222 Chirality : 0.035 0.185 1005 Planarity : 0.004 0.039 1094 Dihedral : 18.236 88.336 2291 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Rotamer: Outliers : 0.84 % Allowed : 28.86 % Favored : 70.30 % 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 aren not related in a simple way. whole: 3.17 (0.29), residues: 787 helix: 2.22 (0.19), residues: 631 sheet: 1.43 (1.15), residues: 23 loop : 1.84 (0.56), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 763 TYR 0.005 0.001 TYR A 504 PHE 0.015 0.001 PHE A 654 TRP 0.012 0.002 TRP A 702 HIS 0.002 0.001 HIS A 155 Details of bonding type rmsd covalent geometry : bond 0.00207 ( 6221) covalent geometry : angle 0.43316 ( 8448) hydrogen bonds : bond 0.12811 ( 520) hydrogen bonds : angle 4.94776 ( 1545) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 27 time to evaluate : 0.176 Fit side-chains outliers start: 5 outliers final: 2 residues processed: 32 average time/residue: 0.4809 time to fit residues: 16.5383 Evaluate side-chains 17 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 15 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 730 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 49 optimal weight: 0.4980 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 38 optimal weight: 0.5980 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 0.5980 chunk 74 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 455 GLN A 723 ASN A 875 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.098434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.077079 restraints weight = 11590.517| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 3.13 r_work: 0.3020 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.1159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6221 Z= 0.136 Angle : 0.460 6.493 8448 Z= 0.239 Chirality : 0.036 0.174 1005 Planarity : 0.004 0.048 1094 Dihedral : 3.696 46.871 881 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Rotamer: Outliers : 4.19 % Allowed : 24.83 % Favored : 70.97 % 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 aren not related in a simple way. whole: 3.72 (0.28), residues: 787 helix: 2.64 (0.19), residues: 641 sheet: 1.53 (1.16), residues: 23 loop : 1.80 (0.60), residues: 123 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 327 TYR 0.007 0.001 TYR A 520 PHE 0.022 0.002 PHE A 165 TRP 0.009 0.001 TRP A 702 HIS 0.002 0.001 HIS A 155 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 6221) covalent geometry : angle 0.45951 ( 8448) hydrogen bonds : bond 0.04222 ( 520) hydrogen bonds : angle 3.59270 ( 1545) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 16 time to evaluate : 0.244 Fit side-chains REVERT: A 490 GLU cc_start: 0.8667 (OUTLIER) cc_final: 0.8191 (tm-30) REVERT: A 844 LEU cc_start: 0.8217 (OUTLIER) cc_final: 0.7965 (tp) outliers start: 25 outliers final: 6 residues processed: 39 average time/residue: 0.3786 time to fit residues: 16.1285 Evaluate side-chains 21 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 13 time to evaluate : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 490 GLU Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 761 ILE Chi-restraints excluded: chain A residue 844 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 27 optimal weight: 0.5980 chunk 41 optimal weight: 1.9990 chunk 71 optimal weight: 0.7980 chunk 51 optimal weight: 4.9990 chunk 18 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 4 optimal weight: 0.7980 chunk 45 optimal weight: 0.6980 chunk 26 optimal weight: 0.6980 chunk 52 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 586 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.096761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.075643 restraints weight = 11588.078| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 3.09 r_work: 0.3018 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 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 : 0.003 0.036 6221 Z= 0.135 Angle : 0.443 6.551 8448 Z= 0.228 Chirality : 0.036 0.187 1005 Planarity : 0.004 0.049 1094 Dihedral : 3.445 46.201 879 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Rotamer: Outliers : 3.36 % Allowed : 24.33 % Favored : 72.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.92 (0.28), residues: 787 helix: 2.79 (0.19), residues: 639 sheet: 1.57 (1.21), residues: 23 loop : 1.80 (0.59), residues: 125 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 327 TYR 0.006 0.001 TYR A 162 PHE 0.020 0.001 PHE A 165 TRP 0.005 0.001 TRP A 702 HIS 0.002 0.001 HIS A 719 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 6221) covalent geometry : angle 0.44310 ( 8448) hydrogen bonds : bond 0.04091 ( 520) hydrogen bonds : angle 3.48361 ( 1545) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 16 time to evaluate : 0.212 Fit side-chains REVERT: A 490 GLU cc_start: 0.8647 (OUTLIER) cc_final: 0.8206 (tm-30) REVERT: A 933 GLU cc_start: 0.8201 (tp30) cc_final: 0.7947 (tp30) outliers start: 20 outliers final: 9 residues processed: 33 average time/residue: 0.4044 time to fit residues: 14.4358 Evaluate side-chains 24 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 14 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 490 GLU Chi-restraints excluded: chain A residue 582 GLU Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 761 ILE Chi-restraints excluded: chain A residue 848 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 10 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 78 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 chunk 24 optimal weight: 0.8980 chunk 46 optimal weight: 0.9980 chunk 14 optimal weight: 0.5980 chunk 40 optimal weight: 0.8980 chunk 16 optimal weight: 0.6980 chunk 28 optimal weight: 0.9990 chunk 75 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 444 GLN A 586 ASN A 756 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.095668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.074576 restraints weight = 11574.232| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 3.08 r_work: 0.2999 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.1640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6221 Z= 0.145 Angle : 0.450 6.730 8448 Z= 0.231 Chirality : 0.036 0.184 1005 Planarity : 0.004 0.048 1094 Dihedral : 3.453 47.049 879 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 2.85 % Allowed : 25.34 % Favored : 71.81 % 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 aren not related in a simple way. whole: 3.96 (0.28), residues: 787 helix: 2.82 (0.19), residues: 639 sheet: 1.70 (1.23), residues: 23 loop : 1.81 (0.59), residues: 125 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 678 TYR 0.007 0.001 TYR A 520 PHE 0.022 0.002 PHE A 165 TRP 0.005 0.001 TRP A 317 HIS 0.002 0.001 HIS A 719 Details of bonding type rmsd covalent geometry : bond 0.00335 ( 6221) covalent geometry : angle 0.44995 ( 8448) hydrogen bonds : bond 0.04086 ( 520) hydrogen bonds : angle 3.44073 ( 1545) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 15 time to evaluate : 0.244 Fit side-chains REVERT: A 490 GLU cc_start: 0.8626 (OUTLIER) cc_final: 0.8243 (tm-30) REVERT: A 933 GLU cc_start: 0.8207 (tp30) cc_final: 0.7924 (tp30) outliers start: 17 outliers final: 8 residues processed: 30 average time/residue: 0.3902 time to fit residues: 12.7767 Evaluate side-chains 23 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 14 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 490 GLU Chi-restraints excluded: chain A residue 582 GLU Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 761 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 45 optimal weight: 0.6980 chunk 55 optimal weight: 0.8980 chunk 8 optimal weight: 0.7980 chunk 46 optimal weight: 2.9990 chunk 54 optimal weight: 0.6980 chunk 1 optimal weight: 0.6980 chunk 52 optimal weight: 0.9980 chunk 44 optimal weight: 0.8980 chunk 41 optimal weight: 0.9990 chunk 42 optimal weight: 0.5980 chunk 47 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 586 ASN A 706 GLN A 756 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.096890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.075493 restraints weight = 11904.514| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 3.24 r_work: 0.2986 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.1722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6221 Z= 0.134 Angle : 0.436 6.413 8448 Z= 0.223 Chirality : 0.036 0.173 1005 Planarity : 0.004 0.048 1094 Dihedral : 3.435 46.486 879 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 4.03 % Allowed : 24.16 % Favored : 71.81 % 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 aren not related in a simple way. whole: 4.04 (0.28), residues: 787 helix: 2.87 (0.19), residues: 639 sheet: 1.60 (1.22), residues: 23 loop : 1.86 (0.59), residues: 125 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 678 TYR 0.006 0.001 TYR A 162 PHE 0.023 0.001 PHE A 165 TRP 0.005 0.001 TRP A 317 HIS 0.002 0.001 HIS A 719 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 6221) covalent geometry : angle 0.43597 ( 8448) hydrogen bonds : bond 0.03991 ( 520) hydrogen bonds : angle 3.40896 ( 1545) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 13 time to evaluate : 0.266 Fit side-chains REVERT: A 490 GLU cc_start: 0.8608 (OUTLIER) cc_final: 0.8221 (tm-30) REVERT: A 676 LEU cc_start: 0.7675 (mt) cc_final: 0.7422 (mp) REVERT: A 933 GLU cc_start: 0.8189 (tp30) cc_final: 0.7929 (tp30) outliers start: 24 outliers final: 11 residues processed: 35 average time/residue: 0.5317 time to fit residues: 19.7493 Evaluate side-chains 25 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 13 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 490 GLU Chi-restraints excluded: chain A residue 582 GLU Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain A residue 761 ILE Chi-restraints excluded: chain A residue 797 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 6 optimal weight: 1.9990 chunk 4 optimal weight: 9.9990 chunk 44 optimal weight: 0.6980 chunk 53 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 75 optimal weight: 0.9980 chunk 27 optimal weight: 0.5980 chunk 46 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 chunk 73 optimal weight: 0.7980 chunk 37 optimal weight: 0.9980 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 586 ASN A 756 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.095256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.074191 restraints weight = 11582.451| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 3.09 r_work: 0.2994 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.1805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6221 Z= 0.148 Angle : 0.447 6.857 8448 Z= 0.228 Chirality : 0.036 0.198 1005 Planarity : 0.004 0.047 1094 Dihedral : 3.473 47.377 879 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 3.86 % Allowed : 23.99 % Favored : 72.15 % 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 aren not related in a simple way. whole: 4.01 (0.28), residues: 787 helix: 2.86 (0.19), residues: 639 sheet: 1.53 (1.21), residues: 23 loop : 1.83 (0.59), residues: 125 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 678 TYR 0.007 0.001 TYR A 520 PHE 0.024 0.001 PHE A 165 TRP 0.005 0.001 TRP A 317 HIS 0.002 0.001 HIS A 719 Details of bonding type rmsd covalent geometry : bond 0.00345 ( 6221) covalent geometry : angle 0.44747 ( 8448) hydrogen bonds : bond 0.04069 ( 520) hydrogen bonds : angle 3.42761 ( 1545) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 14 time to evaluate : 0.195 Fit side-chains REVERT: A 402 GLU cc_start: 0.8825 (OUTLIER) cc_final: 0.8467 (tm-30) REVERT: A 473 ASN cc_start: 0.8424 (t0) cc_final: 0.8128 (t0) REVERT: A 490 GLU cc_start: 0.8637 (OUTLIER) cc_final: 0.8256 (tm-30) REVERT: A 676 LEU cc_start: 0.7733 (mt) cc_final: 0.7467 (mp) REVERT: A 778 ARG cc_start: 0.8253 (OUTLIER) cc_final: 0.7442 (mmp-170) REVERT: A 933 GLU cc_start: 0.8188 (tp30) cc_final: 0.7942 (tp30) outliers start: 23 outliers final: 9 residues processed: 35 average time/residue: 0.3641 time to fit residues: 13.8321 Evaluate side-chains 26 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 14 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 490 GLU Chi-restraints excluded: chain A residue 582 GLU Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 761 ILE Chi-restraints excluded: chain A residue 778 ARG Chi-restraints excluded: chain A residue 797 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 56 optimal weight: 0.5980 chunk 69 optimal weight: 0.9980 chunk 43 optimal weight: 3.9990 chunk 50 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 23 optimal weight: 0.5980 chunk 26 optimal weight: 0.5980 chunk 52 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 chunk 12 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 586 ASN A 756 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.097646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.077191 restraints weight = 11591.109| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 2.98 r_work: 0.3059 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.1848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6221 Z= 0.136 Angle : 0.451 8.418 8448 Z= 0.227 Chirality : 0.036 0.190 1005 Planarity : 0.004 0.048 1094 Dihedral : 3.453 47.019 879 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 3.19 % Allowed : 24.83 % Favored : 71.98 % 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 aren not related in a simple way. whole: 4.07 (0.28), residues: 787 helix: 2.89 (0.19), residues: 639 sheet: 1.51 (1.19), residues: 23 loop : 1.89 (0.60), residues: 125 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 678 TYR 0.010 0.001 TYR A 520 PHE 0.025 0.001 PHE A 165 TRP 0.005 0.001 TRP A 317 HIS 0.002 0.001 HIS A 719 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 6221) covalent geometry : angle 0.45136 ( 8448) hydrogen bonds : bond 0.03989 ( 520) hydrogen bonds : angle 3.39262 ( 1545) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 15 time to evaluate : 0.170 Fit side-chains REVERT: A 402 GLU cc_start: 0.8917 (OUTLIER) cc_final: 0.8539 (tm-30) REVERT: A 473 ASN cc_start: 0.8574 (t0) cc_final: 0.8268 (t0) REVERT: A 490 GLU cc_start: 0.8707 (OUTLIER) cc_final: 0.8345 (tm-30) REVERT: A 676 LEU cc_start: 0.7934 (mt) cc_final: 0.7664 (mp) REVERT: A 778 ARG cc_start: 0.8314 (OUTLIER) cc_final: 0.8112 (mtp180) REVERT: A 933 GLU cc_start: 0.8282 (tp30) cc_final: 0.8028 (tp30) outliers start: 19 outliers final: 14 residues processed: 33 average time/residue: 0.3418 time to fit residues: 12.4031 Evaluate side-chains 32 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 15 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 490 GLU Chi-restraints excluded: chain A residue 582 GLU Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain A residue 761 ILE Chi-restraints excluded: chain A residue 778 ARG Chi-restraints excluded: chain A residue 797 THR Chi-restraints excluded: chain A residue 848 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 61 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 77 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 chunk 71 optimal weight: 0.5980 chunk 9 optimal weight: 0.7980 chunk 70 optimal weight: 0.2980 chunk 74 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 586 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.097931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.077487 restraints weight = 11570.187| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 2.97 r_work: 0.3068 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.1892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6221 Z= 0.127 Angle : 0.441 7.699 8448 Z= 0.222 Chirality : 0.036 0.185 1005 Planarity : 0.004 0.048 1094 Dihedral : 3.437 46.750 879 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 3.02 % Allowed : 25.00 % Favored : 71.98 % 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 aren not related in a simple way. whole: 4.11 (0.28), residues: 787 helix: 2.91 (0.19), residues: 639 sheet: 1.56 (1.19), residues: 23 loop : 1.93 (0.60), residues: 125 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 678 TYR 0.008 0.001 TYR A 520 PHE 0.026 0.001 PHE A 165 TRP 0.005 0.001 TRP A 860 HIS 0.002 0.001 HIS A 719 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 6221) covalent geometry : angle 0.44079 ( 8448) hydrogen bonds : bond 0.03900 ( 520) hydrogen bonds : angle 3.35877 ( 1545) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 17 time to evaluate : 0.225 Fit side-chains REVERT: A 402 GLU cc_start: 0.8941 (OUTLIER) cc_final: 0.8563 (tm-30) REVERT: A 473 ASN cc_start: 0.8623 (t0) cc_final: 0.8324 (t0) REVERT: A 490 GLU cc_start: 0.8700 (OUTLIER) cc_final: 0.8341 (tm-30) REVERT: A 676 LEU cc_start: 0.7948 (mt) cc_final: 0.7719 (mt) REVERT: A 933 GLU cc_start: 0.8284 (tp30) cc_final: 0.8027 (tp30) outliers start: 18 outliers final: 13 residues processed: 34 average time/residue: 0.3031 time to fit residues: 11.4223 Evaluate side-chains 30 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 15 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 490 GLU Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain A residue 761 ILE Chi-restraints excluded: chain A residue 797 THR Chi-restraints excluded: chain A residue 848 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 51 optimal weight: 0.0470 chunk 4 optimal weight: 6.9990 chunk 0 optimal weight: 4.9990 chunk 42 optimal weight: 0.5980 chunk 20 optimal weight: 0.9990 chunk 48 optimal weight: 0.9990 chunk 72 optimal weight: 0.0980 chunk 30 optimal weight: 0.8980 chunk 3 optimal weight: 6.9990 chunk 50 optimal weight: 0.7980 chunk 29 optimal weight: 0.8980 overall best weight: 0.4878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 444 GLN A 586 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.098780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.078397 restraints weight = 11639.522| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 2.99 r_work: 0.3082 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.1928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 6221 Z= 0.112 Angle : 0.432 7.656 8448 Z= 0.218 Chirality : 0.035 0.178 1005 Planarity : 0.004 0.048 1094 Dihedral : 3.420 45.887 879 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 2.35 % Allowed : 25.67 % Favored : 71.98 % 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 aren not related in a simple way. whole: 4.20 (0.28), residues: 787 helix: 2.97 (0.19), residues: 639 sheet: 1.54 (1.20), residues: 23 loop : 1.98 (0.60), residues: 125 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 678 TYR 0.007 0.001 TYR A 520 PHE 0.027 0.001 PHE A 165 TRP 0.005 0.001 TRP A 860 HIS 0.001 0.001 HIS A 719 Details of bonding type rmsd covalent geometry : bond 0.00250 ( 6221) covalent geometry : angle 0.43232 ( 8448) hydrogen bonds : bond 0.03775 ( 520) hydrogen bonds : angle 3.33394 ( 1545) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 17 time to evaluate : 0.248 Fit side-chains REVERT: A 490 GLU cc_start: 0.8694 (OUTLIER) cc_final: 0.8327 (tm-30) REVERT: A 676 LEU cc_start: 0.7920 (mt) cc_final: 0.7668 (mt) REVERT: A 933 GLU cc_start: 0.8386 (tp30) cc_final: 0.8121 (tp30) outliers start: 14 outliers final: 10 residues processed: 29 average time/residue: 0.2317 time to fit residues: 7.8253 Evaluate side-chains 27 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 16 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 490 GLU Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain A residue 848 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 71 optimal weight: 0.5980 chunk 0 optimal weight: 4.9990 chunk 75 optimal weight: 0.3980 chunk 56 optimal weight: 0.9990 chunk 66 optimal weight: 0.9990 chunk 7 optimal weight: 0.8980 chunk 63 optimal weight: 0.9990 chunk 5 optimal weight: 0.7980 chunk 31 optimal weight: 0.8980 chunk 4 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 756 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.097669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.077144 restraints weight = 11678.443| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 3.00 r_work: 0.3058 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.1961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6221 Z= 0.138 Angle : 0.451 7.379 8448 Z= 0.228 Chirality : 0.036 0.188 1005 Planarity : 0.004 0.046 1094 Dihedral : 3.454 47.020 879 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 2.52 % Allowed : 25.50 % Favored : 71.98 % 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 aren not related in a simple way. whole: 4.14 (0.28), residues: 787 helix: 2.93 (0.19), residues: 639 sheet: 1.48 (1.20), residues: 23 loop : 1.96 (0.60), residues: 125 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 678 TYR 0.009 0.001 TYR A 520 PHE 0.027 0.002 PHE A 165 TRP 0.005 0.001 TRP A 317 HIS 0.002 0.001 HIS A 719 Details of bonding type rmsd covalent geometry : bond 0.00318 ( 6221) covalent geometry : angle 0.45093 ( 8448) hydrogen bonds : bond 0.03969 ( 520) hydrogen bonds : angle 3.38243 ( 1545) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 15 time to evaluate : 0.253 Fit side-chains REVERT: A 473 ASN cc_start: 0.8660 (t0) cc_final: 0.8368 (t0) REVERT: A 490 GLU cc_start: 0.8711 (OUTLIER) cc_final: 0.8355 (tm-30) REVERT: A 676 LEU cc_start: 0.7956 (mt) cc_final: 0.7689 (mp) REVERT: A 933 GLU cc_start: 0.8278 (tp30) cc_final: 0.8019 (tp30) outliers start: 15 outliers final: 12 residues processed: 29 average time/residue: 0.2841 time to fit residues: 9.3215 Evaluate side-chains 27 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 14 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 490 GLU Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain A residue 761 ILE Chi-restraints excluded: chain A residue 797 THR Chi-restraints excluded: chain A residue 848 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 53 optimal weight: 0.9980 chunk 39 optimal weight: 0.8980 chunk 8 optimal weight: 0.6980 chunk 36 optimal weight: 0.6980 chunk 22 optimal weight: 0.3980 chunk 64 optimal weight: 0.6980 chunk 76 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 chunk 75 optimal weight: 0.5980 chunk 62 optimal weight: 0.9990 chunk 69 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.098079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.077583 restraints weight = 11605.044| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 2.99 r_work: 0.3067 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.1967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6221 Z= 0.125 Angle : 0.444 7.326 8448 Z= 0.225 Chirality : 0.036 0.183 1005 Planarity : 0.004 0.050 1094 Dihedral : 3.444 46.513 879 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 2.18 % Allowed : 25.84 % Favored : 71.98 % 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 aren not related in a simple way. whole: 4.17 (0.28), residues: 787 helix: 2.98 (0.19), residues: 637 sheet: 1.45 (1.21), residues: 23 loop : 1.86 (0.59), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 678 TYR 0.009 0.001 TYR A 520 PHE 0.027 0.001 PHE A 165 TRP 0.005 0.001 TRP A 860 HIS 0.002 0.001 HIS A 719 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 6221) covalent geometry : angle 0.44425 ( 8448) hydrogen bonds : bond 0.03915 ( 520) hydrogen bonds : angle 3.36690 ( 1545) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1577.38 seconds wall clock time: 27 minutes 38.09 seconds (1658.09 seconds total)