Starting phenix.real_space_refine on Sat Dec 9 02:26:16 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5fn4_3239/12_2023/5fn4_3239.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5fn4_3239/12_2023/5fn4_3239.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5fn4_3239/12_2023/5fn4_3239.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5fn4_3239/12_2023/5fn4_3239.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5fn4_3239/12_2023/5fn4_3239.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5fn4_3239/12_2023/5fn4_3239.pdb" } resolution = 4.0 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= 0.008 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 35 5.16 5 C 6398 2.51 5 N 1596 2.21 5 O 1747 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 52": "NH1" <-> "NH2" Residue "A GLU 155": "OE1" <-> "OE2" Residue "A ARG 233": "NH1" <-> "NH2" Residue "A GLU 245": "OE1" <-> "OE2" Residue "A GLU 348": "OE1" <-> "OE2" Residue "A GLU 364": "OE1" <-> "OE2" Residue "A ARG 391": "NH1" <-> "NH2" Residue "A ARG 496": "NH1" <-> "NH2" Residue "A GLU 500": "OE1" <-> "OE2" Residue "A ARG 539": "NH1" <-> "NH2" Residue "A ARG 622": "NH1" <-> "NH2" Residue "A ARG 626": "NH1" <-> "NH2" Residue "A ARG 629": "NH1" <-> "NH2" Residue "A GLU 650": "OE1" <-> "OE2" Residue "A ARG 652": "NH1" <-> "NH2" Residue "A ARG 657": "NH1" <-> "NH2" Residue "A ARG 659": "NH1" <-> "NH2" Residue "B PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 84": "OE1" <-> "OE2" Residue "C GLU 99": "OE1" <-> "OE2" Residue "C TYR 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 186": "NH1" <-> "NH2" Residue "D GLU 4": "OE1" <-> "OE2" Residue "D GLU 9": "OE1" <-> "OE2" Residue "D GLU 10": "OE1" <-> "OE2" Residue "D ARG 16": "NH1" <-> "NH2" Residue "D GLU 40": "OE1" <-> "OE2" Residue "D GLU 49": "OE1" <-> "OE2" Residue "D ARG 82": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 9776 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 5222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 665, 5222 Classifications: {'peptide': 665} Link IDs: {'PCIS': 2, 'PTRANS': 35, 'TRANS': 627} Chain: "B" Number of atoms: 1714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1714 Classifications: {'peptide': 217} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 210} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 1868 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 1868 Classifications: {'peptide': 243} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 235} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 847 Classifications: {'peptide': 100} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 94} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "G" Number of atoms: 125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 125 Classifications: {'peptide': 25} Link IDs: {'TRANS': 24} Time building chain proxies: 5.45, per 1000 atoms: 0.56 Number of scatterers: 9776 At special positions: 0 Unit cell: (91, 142.8, 103.6, 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 35 16.00 O 1747 8.00 N 1596 7.00 C 6398 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 50 " - pdb=" SG CYS A 62 " distance=2.01 Simple disulfide: pdb=" SG CYS A 140 " - pdb=" SG CYS A 159 " distance=2.04 Simple disulfide: pdb=" SG CYS A 195 " - pdb=" SG CYS A 213 " distance=2.05 Simple disulfide: pdb=" SG CYS A 230 " - pdb=" SG CYS A 248 " distance=2.02 Simple disulfide: pdb=" SG CYS A 586 " - pdb=" SG CYS A 620 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 3.84 Conformation dependent library (CDL) restraints added in 2.3 seconds 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2352 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 6 sheets defined 60.1% alpha, 5.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.01 Creating SS restraints... Processing helix chain 'A' and resid 35 through 40 Processing helix chain 'A' and resid 78 through 87 Processing helix chain 'A' and resid 105 through 113 Processing helix chain 'A' and resid 185 through 200 removed outlier: 4.354A pdb=" N THR A 189 " --> pdb=" O ASP A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 240 removed outlier: 3.862A pdb=" N CYS A 230 " --> pdb=" O SER A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 315 Processing helix chain 'A' and resid 339 through 350 Processing helix chain 'A' and resid 381 through 387 removed outlier: 3.640A pdb=" N ASN A 387 " --> pdb=" O VAL A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 407 removed outlier: 3.829A pdb=" N GLY A 407 " --> pdb=" O LYS A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 431 Processing helix chain 'A' and resid 459 through 464 Processing helix chain 'A' and resid 474 through 478 Processing helix chain 'A' and resid 481 through 502 Processing helix chain 'A' and resid 514 through 527 removed outlier: 3.651A pdb=" N VAL A 518 " --> pdb=" O ASP A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 538 Processing helix chain 'A' and resid 561 through 576 removed outlier: 3.530A pdb=" N VAL A 566 " --> pdb=" O ASN A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 582 through 588 Processing helix chain 'A' and resid 596 through 600 removed outlier: 3.775A pdb=" N TYR A 600 " --> pdb=" O LYS A 597 " (cutoff:3.500A) Processing helix chain 'A' and resid 632 through 637 Processing helix chain 'A' and resid 665 through 693 Processing helix chain 'A' and resid 693 through 698 removed outlier: 3.901A pdb=" N LEU A 697 " --> pdb=" O LYS A 693 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 104 Proline residue: B 88 - end of helix removed outlier: 4.039A pdb=" N SER B 104 " --> pdb=" O ILE B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 190 removed outlier: 3.533A pdb=" N PHE B 177 " --> pdb=" O LEU B 173 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N SER B 178 " --> pdb=" O LEU B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 214 Processing helix chain 'B' and resid 219 through 241 Processing helix chain 'B' and resid 242 through 262 Processing helix chain 'B' and resid 382 through 399 Processing helix chain 'B' and resid 403 through 428 removed outlier: 3.503A pdb=" N THR B 407 " --> pdb=" O ASP B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 452 Processing helix chain 'B' and resid 452 through 464 removed outlier: 4.420A pdb=" N PHE B 456 " --> pdb=" O LEU B 452 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 25 Proline residue: C 16 - end of helix Processing helix chain 'C' and resid 28 through 61 removed outlier: 3.626A pdb=" N THR C 60 " --> pdb=" O LEU C 56 " (cutoff:3.500A) Processing helix chain 'C' and resid 64 through 100 removed outlier: 4.077A pdb=" N GLY C 100 " --> pdb=" O LYS C 96 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 142 removed outlier: 3.864A pdb=" N MET C 117 " --> pdb=" O SER C 113 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N ASN C 136 " --> pdb=" O PHE C 132 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N ILE C 137 " --> pdb=" O SER C 133 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 185 removed outlier: 3.874A pdb=" N THR C 159 " --> pdb=" O TYR C 155 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N THR C 172 " --> pdb=" O ILE C 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 186 through 206 removed outlier: 4.295A pdb=" N LEU C 190 " --> pdb=" O ARG C 186 " (cutoff:3.500A) Processing helix chain 'C' and resid 209 through 212 Processing helix chain 'C' and resid 213 through 232 Processing helix chain 'C' and resid 235 through 243 removed outlier: 3.704A pdb=" N ILE C 239 " --> pdb=" O SER C 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 6 removed outlier: 4.207A pdb=" N ARG D 5 " --> pdb=" O ASN D 2 " (cutoff:3.500A) Processing helix chain 'D' and resid 7 through 23 Processing helix chain 'D' and resid 26 through 43 removed outlier: 4.312A pdb=" N TRP D 36 " --> pdb=" O VAL D 32 " (cutoff:3.500A) Processing helix chain 'D' and resid 49 through 85 Proline residue: D 83 - end of helix Processing helix chain 'D' and resid 86 through 92 Processing helix chain 'G' and resid -1 through 23 Processing sheet with id= AA, first strand: chain 'A' and resid 41 through 44 removed outlier: 4.673A pdb=" N ALA A 658 " --> pdb=" O LEU A 44 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'A' and resid 59 through 60 Processing sheet with id= AC, first strand: chain 'A' and resid 72 through 76 removed outlier: 4.425A pdb=" N GLU A 99 " --> pdb=" O VAL A 76 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'A' and resid 377 through 379 removed outlier: 3.635A pdb=" N SER A 361 " --> pdb=" O VAL A 275 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'A' and resid 577 through 579 removed outlier: 4.172A pdb=" N CYS A 620 " --> pdb=" O VAL A 579 " (cutoff:3.500A) Processing sheet with id= BA, first strand: chain 'B' and resid 193 through 194 removed outlier: 6.858A pdb=" N VAL B 193 " --> pdb=" O PHE D 94 " (cutoff:3.500A) 594 hydrogen bonds defined for protein. 1737 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: 3.26 Time building geometry restraints manager: 4.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1685 1.32 - 1.45: 2759 1.45 - 1.57: 5523 1.57 - 1.70: 8 1.70 - 1.82: 53 Bond restraints: 10028 Sorted by residual: bond pdb=" C LEU C 244 " pdb=" O LEU C 244 " ideal model delta sigma weight residual 1.231 1.380 -0.149 2.00e-02 2.50e+03 5.53e+01 bond pdb=" C HIS C 197 " pdb=" O HIS C 197 " ideal model delta sigma weight residual 1.236 1.304 -0.067 1.15e-02 7.56e+03 3.42e+01 bond pdb=" CA VAL B 87 " pdb=" CB VAL B 87 " ideal model delta sigma weight residual 1.539 1.562 -0.023 5.40e-03 3.43e+04 1.77e+01 bond pdb=" CA VAL B 255 " pdb=" CB VAL B 255 " ideal model delta sigma weight residual 1.540 1.582 -0.042 1.17e-02 7.31e+03 1.31e+01 bond pdb=" N PHE B 86 " pdb=" CA PHE B 86 " ideal model delta sigma weight residual 1.459 1.501 -0.042 1.17e-02 7.31e+03 1.28e+01 ... (remaining 10023 not shown) Histogram of bond angle deviations from ideal: 99.32 - 106.40: 308 106.40 - 113.48: 5136 113.48 - 120.57: 4031 120.57 - 127.65: 4093 127.65 - 134.74: 107 Bond angle restraints: 13675 Sorted by residual: angle pdb=" O ALA G 22 " pdb=" C ALA G 22 " pdb=" N ALA G 23 " ideal model delta sigma weight residual 122.07 109.70 12.37 1.03e+00 9.43e-01 1.44e+02 angle pdb=" O ALA G 21 " pdb=" C ALA G 21 " pdb=" N ALA G 22 " ideal model delta sigma weight residual 122.07 109.73 12.34 1.03e+00 9.43e-01 1.44e+02 angle pdb=" N ILE A 162 " pdb=" CA ILE A 162 " pdb=" C ILE A 162 " ideal model delta sigma weight residual 111.62 118.93 -7.31 7.90e-01 1.60e+00 8.55e+01 angle pdb=" O VAL B 87 " pdb=" C VAL B 87 " pdb=" N PRO B 88 " ideal model delta sigma weight residual 120.42 125.11 -4.69 6.40e-01 2.44e+00 5.38e+01 angle pdb=" CA LEU C 169 " pdb=" C LEU C 169 " pdb=" N LEU C 170 " ideal model delta sigma weight residual 117.07 108.87 8.20 1.14e+00 7.69e-01 5.18e+01 ... (remaining 13670 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.74: 4964 17.74 - 35.47: 643 35.47 - 53.21: 188 53.21 - 70.95: 44 70.95 - 88.68: 12 Dihedral angle restraints: 5851 sinusoidal: 2208 harmonic: 3643 Sorted by residual: dihedral pdb=" CB CYS A 586 " pdb=" SG CYS A 586 " pdb=" SG CYS A 620 " pdb=" CB CYS A 620 " ideal model delta sinusoidal sigma weight residual -86.00 -168.38 82.38 1 1.00e+01 1.00e-02 8.33e+01 dihedral pdb=" CB CYS A 140 " pdb=" SG CYS A 140 " pdb=" SG CYS A 159 " pdb=" CB CYS A 159 " ideal model delta sinusoidal sigma weight residual 93.00 168.51 -75.51 1 1.00e+01 1.00e-02 7.20e+01 dihedral pdb=" CB CYS A 230 " pdb=" SG CYS A 230 " pdb=" SG CYS A 248 " pdb=" CB CYS A 248 " ideal model delta sinusoidal sigma weight residual 93.00 162.50 -69.50 1 1.00e+01 1.00e-02 6.24e+01 ... (remaining 5848 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.120: 1310 0.120 - 0.240: 235 0.240 - 0.360: 30 0.360 - 0.480: 8 0.480 - 0.600: 1 Chirality restraints: 1584 Sorted by residual: chirality pdb=" CA PHE A 302 " pdb=" N PHE A 302 " pdb=" C PHE A 302 " pdb=" CB PHE A 302 " both_signs ideal model delta sigma weight residual False 2.51 1.91 0.60 2.00e-01 2.50e+01 9.00e+00 chirality pdb=" CA PHE A 218 " pdb=" N PHE A 218 " pdb=" C PHE A 218 " pdb=" CB PHE A 218 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.90e+00 chirality pdb=" CA LEU A 312 " pdb=" N LEU A 312 " pdb=" C LEU A 312 " pdb=" CB LEU A 312 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.75e+00 ... (remaining 1581 not shown) Planarity restraints: 1706 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA G 21 " -0.067 2.00e-02 2.50e+03 1.25e-01 1.56e+02 pdb=" C ALA G 21 " 0.216 2.00e-02 2.50e+03 pdb=" O ALA G 21 " -0.080 2.00e-02 2.50e+03 pdb=" N ALA G 22 " -0.069 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA G 22 " -0.067 2.00e-02 2.50e+03 1.25e-01 1.55e+02 pdb=" C ALA G 22 " 0.216 2.00e-02 2.50e+03 pdb=" O ALA G 22 " -0.080 2.00e-02 2.50e+03 pdb=" N ALA G 23 " -0.069 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE B 175 " 0.020 2.00e-02 2.50e+03 4.22e-02 1.78e+01 pdb=" C PHE B 175 " -0.073 2.00e-02 2.50e+03 pdb=" O PHE B 175 " 0.028 2.00e-02 2.50e+03 pdb=" N PHE B 176 " 0.025 2.00e-02 2.50e+03 ... (remaining 1703 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 180 2.69 - 3.24: 10256 3.24 - 3.79: 16234 3.79 - 4.35: 20802 4.35 - 4.90: 32959 Nonbonded interactions: 80431 Sorted by model distance: nonbonded pdb=" O LEU C 35 " pdb=" OG SER C 124 " model vdw 2.131 2.440 nonbonded pdb=" O HIS C 197 " pdb=" OG1 THR C 200 " model vdw 2.252 2.440 nonbonded pdb=" O PHE B 445 " pdb=" OG1 THR B 449 " model vdw 2.267 2.440 nonbonded pdb=" O ALA C 76 " pdb=" OG SER C 79 " model vdw 2.277 2.440 nonbonded pdb=" O ARG A 232 " pdb=" OG SER A 235 " model vdw 2.294 2.440 ... (remaining 80426 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 group one per residue 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: 0.310 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: 0.010 Extract box with map and model: 1.840 Check model and map are aligned: 0.150 Set scattering table: 0.090 Process input model: 29.650 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.050 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5710 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 : 0.010 0.149 10028 Z= 0.644 Angle : 1.713 12.399 13675 Z= 1.236 Chirality : 0.096 0.600 1584 Planarity : 0.009 0.125 1706 Dihedral : 18.066 88.682 3484 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 3.24 % Allowed : 11.98 % Favored : 84.78 % Rotamer: Outliers : 10.51 % Allowed : 14.90 % Favored : 74.59 % Cbeta Deviations : 1.45 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 3.64 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.21), residues: 1235 helix: 1.03 (0.16), residues: 712 sheet: -3.69 (0.40), residues: 110 loop : -3.87 (0.25), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP D 36 HIS 0.017 0.003 HIS A 553 PHE 0.044 0.004 PHE B 176 TYR 0.043 0.004 TYR C 69 ARG 0.006 0.001 ARG A 371 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 316 time to evaluate : 1.040 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 110 outliers final: 34 residues processed: 384 average time/residue: 0.2027 time to fit residues: 108.9857 Evaluate side-chains 243 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 209 time to evaluate : 1.022 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 0 residues processed: 34 average time/residue: 0.0952 time to fit residues: 7.2149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 5.9990 chunk 93 optimal weight: 7.9990 chunk 51 optimal weight: 8.9990 chunk 31 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 49 optimal weight: 4.9990 chunk 96 optimal weight: 1.9990 chunk 37 optimal weight: 0.0010 chunk 58 optimal weight: 2.9990 chunk 71 optimal weight: 4.9990 chunk 111 optimal weight: 3.9990 overall best weight: 2.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 HIS A 305 GLN A 313 GLN ** A 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 367 GLN A 417 ASN ** A 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 478 ASN A 535 GLN A 606 GLN A 612 ASN D 50 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5850 moved from start: 0.3577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 10028 Z= 0.282 Angle : 0.822 10.296 13675 Z= 0.421 Chirality : 0.047 0.198 1584 Planarity : 0.006 0.065 1706 Dihedral : 6.456 36.726 1343 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 16.91 Ramachandran Plot: Outliers : 1.38 % Allowed : 8.18 % Favored : 90.45 % Rotamer: Outliers : 5.16 % Allowed : 21.87 % Favored : 72.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 1.82 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.25), residues: 1235 helix: 2.39 (0.19), residues: 718 sheet: -3.42 (0.35), residues: 125 loop : -3.33 (0.28), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP C 53 HIS 0.013 0.002 HIS A 553 PHE 0.026 0.002 PHE A 302 TYR 0.020 0.002 TYR A 565 ARG 0.005 0.001 ARG C 31 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 237 time to evaluate : 1.086 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 54 outliers final: 24 residues processed: 273 average time/residue: 0.1858 time to fit residues: 75.4943 Evaluate side-chains 205 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 181 time to evaluate : 1.148 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 0.1059 time to fit residues: 6.0109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 62 optimal weight: 4.9990 chunk 34 optimal weight: 8.9990 chunk 92 optimal weight: 6.9990 chunk 76 optimal weight: 7.9990 chunk 30 optimal weight: 10.0000 chunk 111 optimal weight: 9.9990 chunk 120 optimal weight: 0.9990 chunk 99 optimal weight: 10.0000 chunk 110 optimal weight: 0.0980 chunk 38 optimal weight: 10.0000 chunk 89 optimal weight: 3.9990 overall best weight: 3.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 222 HIS A 305 GLN ** A 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 190 ASN B 459 GLN B 464 GLN C 116 GLN C 207 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5921 moved from start: 0.4479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.098 10028 Z= 0.327 Angle : 0.826 19.595 13675 Z= 0.413 Chirality : 0.046 0.293 1584 Planarity : 0.005 0.069 1706 Dihedral : 5.981 36.059 1343 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 19.41 Ramachandran Plot: Outliers : 0.97 % Allowed : 8.10 % Favored : 90.93 % Rotamer: Outliers : 4.87 % Allowed : 22.64 % Favored : 72.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 1.82 % 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: -0.17 (0.25), residues: 1235 helix: 1.93 (0.19), residues: 720 sheet: -3.09 (0.37), residues: 122 loop : -3.15 (0.29), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP C 53 HIS 0.007 0.001 HIS A 553 PHE 0.039 0.002 PHE B 465 TYR 0.028 0.002 TYR B 225 ARG 0.003 0.000 ARG A 539 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 193 time to evaluate : 1.203 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 51 outliers final: 21 residues processed: 225 average time/residue: 0.1817 time to fit residues: 61.8740 Evaluate side-chains 189 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 168 time to evaluate : 1.204 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.0972 time to fit residues: 5.2940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 110 optimal weight: 20.0000 chunk 84 optimal weight: 10.0000 chunk 58 optimal weight: 0.7980 chunk 12 optimal weight: 7.9990 chunk 53 optimal weight: 5.9990 chunk 75 optimal weight: 10.0000 chunk 112 optimal weight: 9.9990 chunk 118 optimal weight: 10.0000 chunk 106 optimal weight: 3.9990 chunk 32 optimal weight: 0.9980 chunk 99 optimal weight: 3.9990 overall best weight: 3.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 190 ASN C 150 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5939 moved from start: 0.4964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 10028 Z= 0.294 Angle : 0.788 12.163 13675 Z= 0.388 Chirality : 0.044 0.235 1584 Planarity : 0.005 0.065 1706 Dihedral : 5.829 37.636 1343 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 19.62 Ramachandran Plot: Outliers : 0.81 % Allowed : 7.94 % Favored : 91.26 % Rotamer: Outliers : 3.06 % Allowed : 24.74 % Favored : 72.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 1.82 % 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: -0.14 (0.25), residues: 1235 helix: 1.89 (0.19), residues: 717 sheet: -2.85 (0.37), residues: 124 loop : -3.05 (0.29), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP C 174 HIS 0.007 0.001 HIS A 553 PHE 0.034 0.002 PHE B 465 TYR 0.027 0.002 TYR A 554 ARG 0.004 0.000 ARG A 626 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 183 time to evaluate : 1.151 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 32 outliers final: 16 residues processed: 207 average time/residue: 0.1738 time to fit residues: 54.6674 Evaluate side-chains 179 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 163 time to evaluate : 1.170 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.1218 time to fit residues: 4.8293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 67 optimal weight: 0.9990 chunk 1 optimal weight: 9.9990 chunk 88 optimal weight: 6.9990 chunk 49 optimal weight: 7.9990 chunk 101 optimal weight: 4.9990 chunk 82 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 60 optimal weight: 10.0000 chunk 106 optimal weight: 6.9990 chunk 30 optimal weight: 7.9990 chunk 40 optimal weight: 0.0050 overall best weight: 1.8002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 355 GLN ** A 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 190 ASN C 116 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5940 moved from start: 0.5324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 10028 Z= 0.237 Angle : 0.764 12.099 13675 Z= 0.374 Chirality : 0.043 0.203 1584 Planarity : 0.005 0.063 1706 Dihedral : 5.554 36.721 1343 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 18.65 Ramachandran Plot: Outliers : 0.81 % Allowed : 7.29 % Favored : 91.90 % Rotamer: Outliers : 2.48 % Allowed : 26.93 % Favored : 70.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 1.82 % 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: -0.14 (0.24), residues: 1235 helix: 1.78 (0.19), residues: 713 sheet: -2.55 (0.39), residues: 116 loop : -2.90 (0.29), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP D 67 HIS 0.005 0.001 HIS C 58 PHE 0.032 0.002 PHE B 465 TYR 0.022 0.002 TYR B 225 ARG 0.003 0.000 ARG A 371 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 188 time to evaluate : 1.162 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 10 residues processed: 205 average time/residue: 0.1725 time to fit residues: 53.7520 Evaluate side-chains 180 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 170 time to evaluate : 1.144 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0985 time to fit residues: 3.1751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 107 optimal weight: 4.9990 chunk 23 optimal weight: 6.9990 chunk 69 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 119 optimal weight: 5.9990 chunk 98 optimal weight: 10.0000 chunk 55 optimal weight: 2.9990 chunk 9 optimal weight: 9.9990 chunk 39 optimal weight: 0.0770 chunk 62 optimal weight: 6.9990 chunk 114 optimal weight: 5.9990 overall best weight: 2.2144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 305 GLN B 190 ASN ** B 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5963 moved from start: 0.5640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 10028 Z= 0.260 Angle : 0.781 11.939 13675 Z= 0.384 Chirality : 0.045 0.323 1584 Planarity : 0.005 0.061 1706 Dihedral : 5.427 35.540 1343 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 20.54 Ramachandran Plot: Outliers : 0.81 % Allowed : 7.53 % Favored : 91.66 % Rotamer: Outliers : 2.01 % Allowed : 27.79 % Favored : 70.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 1.82 % 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: -0.17 (0.25), residues: 1235 helix: 1.71 (0.19), residues: 713 sheet: -2.44 (0.40), residues: 116 loop : -2.84 (0.29), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP C 174 HIS 0.005 0.001 HIS C 58 PHE 0.040 0.002 PHE C 132 TYR 0.023 0.002 TYR B 389 ARG 0.012 0.000 ARG D 59 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 177 time to evaluate : 1.030 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 13 residues processed: 187 average time/residue: 0.1740 time to fit residues: 49.4098 Evaluate side-chains 178 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 165 time to evaluate : 1.119 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.0998 time to fit residues: 3.7224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 13 optimal weight: 9.9990 chunk 67 optimal weight: 5.9990 chunk 86 optimal weight: 5.9990 chunk 100 optimal weight: 2.9990 chunk 66 optimal weight: 8.9990 chunk 118 optimal weight: 9.9990 chunk 74 optimal weight: 6.9990 chunk 72 optimal weight: 10.0000 chunk 54 optimal weight: 6.9990 chunk 73 optimal weight: 0.9990 chunk 47 optimal weight: 9.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 ASN ** A 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 190 ASN ** B 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 116 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5995 moved from start: 0.5829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 10028 Z= 0.370 Angle : 0.802 11.647 13675 Z= 0.406 Chirality : 0.045 0.198 1584 Planarity : 0.005 0.065 1706 Dihedral : 5.586 36.711 1343 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 24.72 Ramachandran Plot: Outliers : 0.73 % Allowed : 8.42 % Favored : 90.85 % Rotamer: Outliers : 2.10 % Allowed : 29.13 % Favored : 68.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 1.82 % 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: -0.36 (0.24), residues: 1235 helix: 1.48 (0.19), residues: 715 sheet: -2.28 (0.41), residues: 116 loop : -2.87 (0.30), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP C 174 HIS 0.008 0.002 HIS A 102 PHE 0.028 0.002 PHE B 465 TYR 0.032 0.002 TYR B 181 ARG 0.011 0.001 ARG D 59 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 170 time to evaluate : 1.168 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 16 residues processed: 181 average time/residue: 0.1763 time to fit residues: 48.6500 Evaluate side-chains 177 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 161 time to evaluate : 1.150 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.1093 time to fit residues: 4.7508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 70 optimal weight: 0.9990 chunk 35 optimal weight: 10.0000 chunk 23 optimal weight: 9.9990 chunk 22 optimal weight: 5.9990 chunk 75 optimal weight: 6.9990 chunk 80 optimal weight: 4.9990 chunk 58 optimal weight: 5.9990 chunk 11 optimal weight: 9.9990 chunk 93 optimal weight: 4.9990 chunk 107 optimal weight: 2.9990 chunk 113 optimal weight: 1.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 ASN ** A 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 190 ASN ** B 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5984 moved from start: 0.6008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 10028 Z= 0.299 Angle : 0.786 12.923 13675 Z= 0.391 Chirality : 0.044 0.193 1584 Planarity : 0.005 0.068 1706 Dihedral : 5.500 34.039 1343 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 22.68 Ramachandran Plot: Outliers : 0.73 % Allowed : 8.42 % Favored : 90.85 % Rotamer: Outliers : 1.15 % Allowed : 30.47 % Favored : 68.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 1.82 % 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: -0.34 (0.24), residues: 1235 helix: 1.46 (0.19), residues: 719 sheet: -2.20 (0.42), residues: 116 loop : -2.84 (0.30), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP C 174 HIS 0.006 0.001 HIS C 58 PHE 0.030 0.002 PHE B 465 TYR 0.026 0.002 TYR B 181 ARG 0.009 0.000 ARG D 59 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 181 time to evaluate : 1.022 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 5 residues processed: 188 average time/residue: 0.1787 time to fit residues: 51.4263 Evaluate side-chains 169 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 164 time to evaluate : 1.192 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0954 time to fit residues: 2.3970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 3.9990 chunk 110 optimal weight: 20.0000 chunk 113 optimal weight: 0.8980 chunk 66 optimal weight: 0.4980 chunk 48 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 chunk 99 optimal weight: 3.9990 chunk 104 optimal weight: 0.7980 chunk 72 optimal weight: 0.9990 chunk 116 optimal weight: 6.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 190 ASN ** D 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5970 moved from start: 0.6171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 10028 Z= 0.214 Angle : 0.799 15.061 13675 Z= 0.385 Chirality : 0.045 0.269 1584 Planarity : 0.005 0.066 1706 Dihedral : 5.350 36.156 1343 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 20.02 Ramachandran Plot: Outliers : 0.73 % Allowed : 7.21 % Favored : 92.06 % Rotamer: Outliers : 0.67 % Allowed : 32.09 % Favored : 67.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 1.82 % 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: -0.23 (0.24), residues: 1235 helix: 1.58 (0.19), residues: 707 sheet: -2.05 (0.43), residues: 116 loop : -2.79 (0.30), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP C 53 HIS 0.004 0.001 HIS C 58 PHE 0.048 0.002 PHE C 205 TYR 0.026 0.001 TYR B 181 ARG 0.007 0.000 ARG D 59 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 188 time to evaluate : 1.214 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 4 residues processed: 189 average time/residue: 0.1908 time to fit residues: 53.7571 Evaluate side-chains 168 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 164 time to evaluate : 1.147 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1051 time to fit residues: 2.2516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 71 optimal weight: 10.0000 chunk 55 optimal weight: 6.9990 chunk 81 optimal weight: 6.9990 chunk 122 optimal weight: 10.0000 chunk 112 optimal weight: 10.0000 chunk 97 optimal weight: 20.0000 chunk 10 optimal weight: 9.9990 chunk 75 optimal weight: 4.9990 chunk 59 optimal weight: 0.0970 chunk 77 optimal weight: 5.9990 chunk 103 optimal weight: 0.9990 overall best weight: 3.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 GLN ** A 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 190 ASN ** B 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6005 moved from start: 0.6294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 10028 Z= 0.343 Angle : 0.825 12.592 13675 Z= 0.412 Chirality : 0.046 0.256 1584 Planarity : 0.006 0.074 1706 Dihedral : 5.521 34.107 1343 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 24.52 Ramachandran Plot: Outliers : 0.73 % Allowed : 7.94 % Favored : 91.34 % Rotamer: Outliers : 0.67 % Allowed : 32.38 % Favored : 66.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 1.82 % 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: -0.39 (0.25), residues: 1235 helix: 1.33 (0.19), residues: 725 sheet: -2.06 (0.43), residues: 116 loop : -2.79 (0.31), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP C 53 HIS 0.006 0.001 HIS A 102 PHE 0.027 0.002 PHE B 465 TYR 0.021 0.002 TYR B 466 ARG 0.011 0.001 ARG D 82 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 171 time to evaluate : 1.094 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 4 residues processed: 174 average time/residue: 0.1722 time to fit residues: 45.8380 Evaluate side-chains 170 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 166 time to evaluate : 1.108 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0943 time to fit residues: 2.1984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 29 optimal weight: 3.9990 chunk 89 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 chunk 27 optimal weight: 3.9990 chunk 97 optimal weight: 20.0000 chunk 40 optimal weight: 8.9990 chunk 100 optimal weight: 0.9990 chunk 12 optimal weight: 0.0970 chunk 18 optimal weight: 0.9990 chunk 85 optimal weight: 9.9990 chunk 5 optimal weight: 0.9980 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 190 ASN ** B 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.068306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.057986 restraints weight = 48776.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.059670 restraints weight = 27659.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.060792 restraints weight = 18084.231| |-----------------------------------------------------------------------------| r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.6529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 10028 Z= 0.228 Angle : 0.814 14.596 13675 Z= 0.394 Chirality : 0.045 0.226 1584 Planarity : 0.005 0.066 1706 Dihedral : 5.326 34.531 1343 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 20.48 Ramachandran Plot: Outliers : 0.65 % Allowed : 7.53 % Favored : 91.82 % Rotamer: Outliers : 0.38 % Allowed : 33.14 % Favored : 66.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 1.82 % 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: -0.37 (0.25), residues: 1235 helix: 1.36 (0.19), residues: 724 sheet: -2.20 (0.42), residues: 125 loop : -2.75 (0.31), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP C 53 HIS 0.004 0.001 HIS C 58 PHE 0.030 0.002 PHE A 302 TYR 0.021 0.001 TYR B 181 ARG 0.010 0.000 ARG D 82 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2003.52 seconds wall clock time: 37 minutes 30.83 seconds (2250.83 seconds total)