Starting phenix.real_space_refine (version: dev) on Thu May 12 20:44:29 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mhy_23836/05_2022/7mhy_23836_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mhy_23836/05_2022/7mhy_23836.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mhy_23836/05_2022/7mhy_23836_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mhy_23836/05_2022/7mhy_23836_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mhy_23836/05_2022/7mhy_23836_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mhy_23836/05_2022/7mhy_23836.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mhy_23836/05_2022/7mhy_23836.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mhy_23836/05_2022/7mhy_23836_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mhy_23836/05_2022/7mhy_23836_updated.pdb" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.402 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A PHE 331": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/modules/chem_data/mon_lib" Total number of atoms: 7904 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 491, 4003 Classifications: {'peptide': 491} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 16, 'TRANS': 474} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 21 Chain: "M" Number of atoms: 887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 887 Classifications: {'peptide': 118} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 3, 'TRANS': 114} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "N" Number of atoms: 812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 812 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 5, 'TRANS': 102, 'PCIS': 1} Chain breaks: 1 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 27 Chain: "O" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 805 Classifications: {'peptide': 100} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 3, 'TRANS': 96} Chain breaks: 3 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "P" Number of atoms: 683 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 683 Classifications: {'peptide': 94} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 3, 'TRANS': 88, 'PCIS': 2} Chain breaks: 3 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 20 Chain: "A" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 714 Unusual residues: {'PKZ': 3, 'HEM': 1, 'AJP': 14} Classifications: {'undetermined': 18, 'water': 15} Link IDs: {None: 32} Unresolved non-hydrogen bonds: 320 Unresolved non-hydrogen angles: 483 Unresolved non-hydrogen dihedrals: 621 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'PKZ:plan-3': 1, 'PKZ:plan-2': 1, 'PKZ:plan-1': 1, 'PKZ:plan-5': 1, 'PKZ:plan-4': 1} Unresolved non-hydrogen planarities: 26 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2668 SG CYS A 324 41.775 58.564 80.769 1.00 29.38 S Time building chain proxies: 5.09, per 1000 atoms: 0.64 Number of scatterers: 7904 At special positions: 0 Unit cell: (74.48, 90.972, 144.704, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 1 26.01 S 48 16.00 P 6 15.00 O 1408 8.00 N 1177 7.00 C 5264 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS M 41 " - pdb=" SG CYS M 115 " distance=2.03 Simple disulfide: pdb=" SG CYS N 42 " - pdb=" SG CYS N 112 " distance=2.05 Simple disulfide: pdb=" SG CYS O 41 " - pdb=" SG CYS O 115 " distance=2.03 Simple disulfide: pdb=" SG CYS P 42 " - pdb=" SG CYS P 112 " distance=2.04 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.06 Conformation dependent library (CDL) restraints added in 1.1 seconds 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1676 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 28 helices and 11 sheets defined 42.1% alpha, 16.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.86 Creating SS restraints... Processing helix chain 'A' and resid 4 through 28 Processing helix chain 'A' and resid 33 through 37 Processing helix chain 'A' and resid 59 through 69 Processing helix chain 'A' and resid 71 through 88 Processing helix chain 'A' and resid 93 through 130 removed outlier: 8.291A pdb=" N THR A 111 " --> pdb=" O CYS A 107 " (cutoff:3.500A) Proline residue: A 112 - end of helix removed outlier: 4.428A pdb=" N PHE A 130 " --> pdb=" O CYS A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 148 removed outlier: 3.714A pdb=" N LEU A 147 " --> pdb=" O LEU A 143 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ARG A 148 " --> pdb=" O LEU A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 159 removed outlier: 3.743A pdb=" N TRP A 159 " --> pdb=" O VAL A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 188 removed outlier: 4.176A pdb=" N LEU A 178 " --> pdb=" O THR A 174 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N TYR A 179 " --> pdb=" O VAL A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 198 No H-bonds generated for 'chain 'A' and resid 196 through 198' Processing helix chain 'A' and resid 201 through 208 Processing helix chain 'A' and resid 211 through 213 No H-bonds generated for 'chain 'A' and resid 211 through 213' Processing helix chain 'A' and resid 222 through 229 Processing helix chain 'A' and resid 237 through 264 removed outlier: 3.502A pdb=" N ALA A 245 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU A 246 " --> pdb=" O CYS A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 271 Processing helix chain 'A' and resid 274 through 277 No H-bonds generated for 'chain 'A' and resid 274 through 277' Processing helix chain 'A' and resid 282 through 314 Proline residue: A 307 - end of helix Processing helix chain 'A' and resid 325 through 327 No H-bonds generated for 'chain 'A' and resid 325 through 327' Processing helix chain 'A' and resid 331 through 337 Processing helix chain 'A' and resid 340 through 349 Processing helix chain 'A' and resid 351 through 354 No H-bonds generated for 'chain 'A' and resid 351 through 354' Processing helix chain 'A' and resid 361 through 378 Processing helix chain 'A' and resid 383 through 406 Processing helix chain 'A' and resid 409 through 418 Processing helix chain 'A' and resid 421 through 448 removed outlier: 3.775A pdb=" N CYS A 434 " --> pdb=" O ALA A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 461 Processing helix chain 'A' and resid 468 through 489 removed outlier: 4.602A pdb=" N THR A 489 " --> pdb=" O ALA A 485 " (cutoff:3.500A) Processing helix chain 'M' and resid 107 through 109 No H-bonds generated for 'chain 'M' and resid 107 through 109' Processing helix chain 'O' and resid 81 through 83 No H-bonds generated for 'chain 'O' and resid 81 through 83' Processing sheet with id= A, first strand: chain 'A' and resid 42 through 44 Processing sheet with id= B, first strand: chain 'M' and resid 22 through 25 Processing sheet with id= C, first strand: chain 'M' and resid 29 through 31 removed outlier: 3.789A pdb=" N GLY M 68 " --> pdb=" O TRP M 55 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N LYS M 57 " --> pdb=" O TRP M 66 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N TRP M 66 " --> pdb=" O LYS M 57 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'M' and resid 116 through 118 Processing sheet with id= E, first strand: chain 'N' and resid 23 through 26 Processing sheet with id= F, first strand: chain 'N' and resid 29 through 31 removed outlier: 6.465A pdb=" N LYS N 127 " --> pdb=" O LEU N 30 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'N' and resid 109 through 114 removed outlier: 6.176A pdb=" N LEU N 61 " --> pdb=" O LEU N 70 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N LEU N 70 " --> pdb=" O LEU N 61 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'O' and resid 22 through 25 Processing sheet with id= I, first strand: chain 'O' and resid 77 through 79 removed outlier: 6.815A pdb=" N TRP O 55 " --> pdb=" O MET O 67 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N TRP O 69 " --> pdb=" O MET O 53 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N MET O 53 " --> pdb=" O TRP O 69 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N TYR O 127 " --> pdb=" O ARG O 117 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'P' and resid 23 through 26 removed outlier: 3.547A pdb=" N SER P 41 " --> pdb=" O THR P 26 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'P' and resid 109 through 114 removed outlier: 3.820A pdb=" N TRP P 59 " --> pdb=" O ILE P 72 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ILE P 72 " --> pdb=" O TRP P 59 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N LEU P 61 " --> pdb=" O LEU P 70 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N LEU P 70 " --> pdb=" O LEU P 61 " (cutoff:3.500A) 355 hydrogen bonds defined for protein. 1020 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: 2.42 Time building geometry restraints manager: 3.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.37: 2811 1.37 - 1.54: 5170 1.54 - 1.71: 144 1.71 - 1.88: 74 1.88 - 2.04: 4 Bond restraints: 8203 Sorted by residual: bond pdb=" CBX AJP A 505 " pdb=" OAU AJP A 505 " ideal model delta sigma weight residual 0.000 1.434 -1.434 2.00e-02 2.50e+03 5.14e+03 bond pdb=" CBH AJP A 506 " pdb=" OBG AJP A 506 " ideal model delta sigma weight residual 0.034 1.434 -1.400 2.00e-02 2.50e+03 4.90e+03 bond pdb=" CBH AJP A 516 " pdb=" OBG AJP A 516 " ideal model delta sigma weight residual 0.034 1.433 -1.399 2.00e-02 2.50e+03 4.89e+03 bond pdb=" CBH AJP A 514 " pdb=" OBG AJP A 514 " ideal model delta sigma weight residual 0.034 1.432 -1.398 2.00e-02 2.50e+03 4.89e+03 bond pdb=" CBH AJP A 515 " pdb=" OBG AJP A 515 " ideal model delta sigma weight residual 0.034 1.432 -1.398 2.00e-02 2.50e+03 4.89e+03 ... (remaining 8198 not shown) Histogram of bond angle deviations from ideal: 88.41 - 105.85: 287 105.85 - 123.29: 10594 123.29 - 140.73: 480 140.73 - 158.16: 0 158.16 - 175.60: 2 Bond angle restraints: 11363 Sorted by residual: angle pdb=" CAW AJP A 511 " pdb=" CBF AJP A 511 " pdb=" CBE AJP A 511 " ideal model delta sigma weight residual 163.43 114.66 48.77 3.00e+00 1.11e-01 2.64e+02 angle pdb=" CAW AJP A 518 " pdb=" CBF AJP A 518 " pdb=" CBE AJP A 518 " ideal model delta sigma weight residual 163.43 114.66 48.77 3.00e+00 1.11e-01 2.64e+02 angle pdb=" CAW AJP A 512 " pdb=" CBF AJP A 512 " pdb=" CBE AJP A 512 " ideal model delta sigma weight residual 163.43 114.74 48.69 3.00e+00 1.11e-01 2.63e+02 angle pdb=" CAW AJP A 509 " pdb=" CBF AJP A 509 " pdb=" CBE AJP A 509 " ideal model delta sigma weight residual 163.43 114.80 48.63 3.00e+00 1.11e-01 2.63e+02 angle pdb=" CAW AJP A 510 " pdb=" CBF AJP A 510 " pdb=" CBE AJP A 510 " ideal model delta sigma weight residual 163.43 114.91 48.52 3.00e+00 1.11e-01 2.62e+02 ... (remaining 11358 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.68: 5016 33.68 - 67.37: 151 67.37 - 101.05: 74 101.05 - 134.73: 49 134.73 - 168.41: 2 Dihedral angle restraints: 5292 sinusoidal: 2659 harmonic: 2633 Sorted by residual: dihedral pdb=" C VAL N 75 " pdb=" N VAL N 75 " pdb=" CA VAL N 75 " pdb=" CB VAL N 75 " ideal model delta harmonic sigma weight residual -122.00 -137.82 15.82 0 2.50e+00 1.60e-01 4.00e+01 dihedral pdb=" N VAL N 75 " pdb=" C VAL N 75 " pdb=" CA VAL N 75 " pdb=" CB VAL N 75 " ideal model delta harmonic sigma weight residual 123.40 137.15 -13.75 0 2.50e+00 1.60e-01 3.02e+01 dihedral pdb=" CCX AJP A 510 " pdb=" CCZ AJP A 510 " pdb=" OCY AJP A 510 " pdb=" CDA AJP A 510 " ideal model delta sinusoidal sigma weight residual 133.20 -58.39 -168.41 1 3.00e+01 1.11e-03 2.11e+01 ... (remaining 5289 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.299: 1107 0.299 - 0.598: 16 0.598 - 0.897: 0 0.897 - 1.196: 0 1.196 - 1.495: 14 Chirality restraints: 1137 Sorted by residual: chirality pdb=" CBN AJP A 511 " pdb=" CBM AJP A 511 " pdb=" CBO AJP A 511 " pdb=" CCJ AJP A 511 " both_signs ideal model delta sigma weight residual True 1.53 -3.02 -1.49 2.00e-01 2.50e+01 5.59e+01 chirality pdb=" CBN AJP A 516 " pdb=" CBM AJP A 516 " pdb=" CBO AJP A 516 " pdb=" CCJ AJP A 516 " both_signs ideal model delta sigma weight residual True 1.53 -3.02 -1.49 2.00e-01 2.50e+01 5.55e+01 chirality pdb=" CBN AJP A 506 " pdb=" CBM AJP A 506 " pdb=" CBO AJP A 506 " pdb=" CCJ AJP A 506 " both_signs ideal model delta sigma weight residual True 1.53 -3.01 -1.48 2.00e-01 2.50e+01 5.50e+01 ... (remaining 1134 not shown) Planarity restraints: 1243 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C3P PKZ A 502 " -0.086 2.00e-02 2.50e+03 7.10e-02 6.30e+01 pdb=" C5P PKZ A 502 " 0.024 2.00e-02 2.50e+03 pdb=" C6P PKZ A 502 " -0.065 2.00e-02 2.50e+03 pdb=" N4P PKZ A 502 " 0.113 2.00e-02 2.50e+03 pdb=" O5P PKZ A 502 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 271 " -0.033 2.00e-02 2.50e+03 2.82e-02 1.59e+01 pdb=" CG TYR A 271 " 0.069 2.00e-02 2.50e+03 pdb=" CD1 TYR A 271 " -0.018 2.00e-02 2.50e+03 pdb=" CD2 TYR A 271 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR A 271 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR A 271 " -0.012 2.00e-02 2.50e+03 pdb=" CZ TYR A 271 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR A 271 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C7P PKZ A 502 " 0.033 2.00e-02 2.50e+03 2.71e-02 9.15e+00 pdb=" C9P PKZ A 502 " -0.010 2.00e-02 2.50e+03 pdb=" CAP PKZ A 502 " 0.025 2.00e-02 2.50e+03 pdb=" N8P PKZ A 502 " -0.043 2.00e-02 2.50e+03 pdb=" O9P PKZ A 502 " -0.005 2.00e-02 2.50e+03 ... (remaining 1240 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 290 2.71 - 3.26: 7463 3.26 - 3.80: 12819 3.80 - 4.35: 16387 4.35 - 4.90: 27579 Nonbonded interactions: 64538 Sorted by model distance: nonbonded pdb=" OH TYR A 210 " pdb=" OD2 ASP A 314 " model vdw 2.160 2.440 nonbonded pdb=" O MET A 328 " pdb=" OH TYR A 479 " model vdw 2.265 2.440 nonbonded pdb=" O2B PKZ A 502 " pdb=" O7A PKZ A 502 " model vdw 2.278 2.440 nonbonded pdb=" O LEU A 143 " pdb=" OG1 THR A 146 " model vdw 2.327 2.440 nonbonded pdb=" O SER N 116 " pdb=" OG SER N 116 " model vdw 2.336 2.440 ... (remaining 64533 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 Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Fe 1 7.16 5 P 6 5.49 5 S 48 5.16 5 C 5264 2.51 5 N 1177 2.21 5 O 1408 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 2.640 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: 14.380 Check model and map are aligned: 0.100 Convert atoms to be neutral: 0.060 Process input model: 25.290 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:15.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8786 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 : 0.115 1.434 8203 Z= 6.363 Angle : 2.807 48.775 11363 Z= 0.987 Chirality : 0.183 1.495 1137 Planarity : 0.005 0.071 1243 Dihedral : 22.850 168.413 3604 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer Outliers : 0.54 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.28), residues: 888 helix: 1.92 (0.26), residues: 385 sheet: 0.61 (0.37), residues: 198 loop : -0.92 (0.33), residues: 305 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 152 time to evaluate : 0.889 Fit side-chains TARDY: cannot create tardy model for: "SER A 29 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE A 462 " (corrupted residue). Skipping it. outliers start: 4 outliers final: 3 residues processed: 155 average time/residue: 1.0059 time to fit residues: 166.9267 Evaluate side-chains 147 residues out of total 788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 144 time to evaluate : 0.899 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 3 residues processed: 0 time to fit residues: 1.1019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 75 optimal weight: 4.9990 chunk 67 optimal weight: 4.9990 chunk 37 optimal weight: 0.6980 chunk 23 optimal weight: 5.9990 chunk 45 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 chunk 69 optimal weight: 0.0040 chunk 26 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 overall best weight: 0.7396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 488 GLN ** N 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8774 moved from start: 0.0764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.063 8203 Z= 0.292 Angle : 1.378 20.612 11363 Z= 0.518 Chirality : 0.040 0.172 1137 Planarity : 0.004 0.040 1243 Dihedral : 25.681 170.482 2112 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 40.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer Outliers : 2.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.28), residues: 888 helix: 2.01 (0.26), residues: 383 sheet: 0.55 (0.36), residues: 201 loop : -0.94 (0.33), residues: 304 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 137 time to evaluate : 0.808 Fit side-chains TARDY: cannot create tardy model for: "SER A 29 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE A 462 " (corrupted residue). Skipping it. outliers start: 16 outliers final: 10 residues processed: 147 average time/residue: 0.9583 time to fit residues: 151.4546 Evaluate side-chains 145 residues out of total 788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 135 time to evaluate : 0.865 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 9 residues processed: 1 average time/residue: 0.1205 time to fit residues: 1.3744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 44 optimal weight: 2.9990 chunk 25 optimal weight: 0.6980 chunk 67 optimal weight: 0.6980 chunk 55 optimal weight: 0.4980 chunk 22 optimal weight: 0.9980 chunk 80 optimal weight: 3.9990 chunk 87 optimal weight: 0.8980 chunk 72 optimal weight: 4.9990 chunk 27 optimal weight: 0.2980 chunk 64 optimal weight: 2.9990 chunk 79 optimal weight: 4.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 54 ASN ** N 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8765 moved from start: 0.0895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.052 8203 Z= 0.250 Angle : 1.232 19.275 11363 Z= 0.469 Chirality : 0.040 0.175 1137 Planarity : 0.004 0.039 1243 Dihedral : 24.633 172.006 2112 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 40.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer Outliers : 2.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.28), residues: 888 helix: 2.07 (0.26), residues: 383 sheet: 0.54 (0.36), residues: 201 loop : -0.94 (0.33), residues: 304 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 132 time to evaluate : 0.847 Fit side-chains TARDY: cannot create tardy model for: "SER A 29 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE A 462 " (corrupted residue). Skipping it. outliers start: 19 outliers final: 14 residues processed: 142 average time/residue: 0.9935 time to fit residues: 151.1473 Evaluate side-chains 144 residues out of total 788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 130 time to evaluate : 0.760 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 10 residues processed: 4 average time/residue: 0.5261 time to fit residues: 3.3567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 60 optimal weight: 0.9980 chunk 42 optimal weight: 0.7980 chunk 8 optimal weight: 5.9990 chunk 38 optimal weight: 0.7980 chunk 54 optimal weight: 3.9990 chunk 81 optimal weight: 10.0000 chunk 86 optimal weight: 0.9990 chunk 77 optimal weight: 5.9990 chunk 23 optimal weight: 5.9990 chunk 71 optimal weight: 0.7980 chunk 48 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 54 ASN ** N 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8761 moved from start: 0.1019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.040 8203 Z= 0.255 Angle : 1.148 17.661 11363 Z= 0.443 Chirality : 0.041 0.166 1137 Planarity : 0.004 0.037 1243 Dihedral : 24.370 170.420 2112 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 40.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer Outliers : 2.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.28), residues: 888 helix: 2.16 (0.26), residues: 383 sheet: 0.57 (0.36), residues: 201 loop : -0.96 (0.33), residues: 304 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 134 time to evaluate : 0.849 Fit side-chains TARDY: cannot create tardy model for: "SER A 29 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE A 462 " (corrupted residue). Skipping it. outliers start: 19 outliers final: 16 residues processed: 146 average time/residue: 0.9313 time to fit residues: 146.1041 Evaluate side-chains 148 residues out of total 788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 132 time to evaluate : 0.816 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 11 residues processed: 5 average time/residue: 0.2988 time to fit residues: 2.9233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 1 optimal weight: 0.6980 chunk 64 optimal weight: 3.9990 chunk 35 optimal weight: 5.9990 chunk 73 optimal weight: 0.2980 chunk 59 optimal weight: 0.2980 chunk 0 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 77 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 54 ASN N 77 ASN ** N 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8757 moved from start: 0.1052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 8203 Z= 0.220 Angle : 1.116 17.175 11363 Z= 0.429 Chirality : 0.040 0.167 1137 Planarity : 0.004 0.038 1243 Dihedral : 24.299 170.206 2112 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 41.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer Outliers : 2.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.28), residues: 888 helix: 2.20 (0.26), residues: 383 sheet: 0.57 (0.36), residues: 201 loop : -0.97 (0.33), residues: 304 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 134 time to evaluate : 0.859 Fit side-chains TARDY: cannot create tardy model for: "SER A 29 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE A 462 " (corrupted residue). Skipping it. outliers start: 18 outliers final: 15 residues processed: 146 average time/residue: 0.9606 time to fit residues: 151.1012 Evaluate side-chains 148 residues out of total 788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 133 time to evaluate : 0.842 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 12 residues processed: 3 average time/residue: 0.1089 time to fit residues: 1.5373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 50 optimal weight: 0.7980 chunk 21 optimal weight: 2.9990 chunk 86 optimal weight: 6.9990 chunk 71 optimal weight: 20.0000 chunk 39 optimal weight: 0.6980 chunk 7 optimal weight: 2.9990 chunk 28 optimal weight: 5.9990 chunk 45 optimal weight: 0.9980 chunk 83 optimal weight: 0.9990 chunk 9 optimal weight: 0.1980 chunk 49 optimal weight: 3.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 54 ASN ** N 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8755 moved from start: 0.1126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.067 8203 Z= 0.265 Angle : 1.092 16.428 11363 Z= 0.422 Chirality : 0.040 0.165 1137 Planarity : 0.004 0.035 1243 Dihedral : 24.067 170.103 2112 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 40.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer Outliers : 2.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.28), residues: 888 helix: 2.22 (0.26), residues: 383 sheet: 0.58 (0.36), residues: 201 loop : -0.96 (0.33), residues: 304 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 133 time to evaluate : 0.861 Fit side-chains TARDY: cannot create tardy model for: "SER A 29 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE A 462 " (corrupted residue). Skipping it. outliers start: 19 outliers final: 17 residues processed: 147 average time/residue: 0.9172 time to fit residues: 145.1204 Evaluate side-chains 150 residues out of total 788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 133 time to evaluate : 0.910 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 12 residues processed: 5 average time/residue: 0.2927 time to fit residues: 2.8911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 62 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 72 optimal weight: 0.6980 chunk 85 optimal weight: 0.3980 chunk 53 optimal weight: 2.9990 chunk 52 optimal weight: 0.8980 chunk 39 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 54 ASN N 77 ASN ** N 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8753 moved from start: 0.1141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 8203 Z= 0.217 Angle : 1.075 16.212 11363 Z= 0.415 Chirality : 0.040 0.166 1137 Planarity : 0.004 0.035 1243 Dihedral : 23.973 170.040 2112 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 41.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer Outliers : 2.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.28), residues: 888 helix: 2.25 (0.26), residues: 382 sheet: 0.58 (0.36), residues: 201 loop : -0.94 (0.33), residues: 305 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 132 time to evaluate : 0.887 Fit side-chains TARDY: cannot create tardy model for: "SER A 29 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE A 462 " (corrupted residue). Skipping it. outliers start: 15 outliers final: 14 residues processed: 143 average time/residue: 0.9605 time to fit residues: 147.7204 Evaluate side-chains 146 residues out of total 788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 132 time to evaluate : 0.806 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 11 residues processed: 3 average time/residue: 0.1265 time to fit residues: 1.7196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 16 optimal weight: 0.0980 chunk 54 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 chunk 7 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 chunk 82 optimal weight: 4.9990 chunk 74 optimal weight: 0.3980 chunk 79 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 54 ASN N 77 ASN ** N 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8753 moved from start: 0.1146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.037 8203 Z= 0.226 Angle : 1.073 16.147 11363 Z= 0.414 Chirality : 0.040 0.165 1137 Planarity : 0.004 0.035 1243 Dihedral : 23.951 170.057 2112 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 41.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer Outliers : 2.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.28), residues: 888 helix: 2.27 (0.26), residues: 381 sheet: 0.58 (0.36), residues: 201 loop : -0.93 (0.33), residues: 306 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 131 time to evaluate : 0.854 Fit side-chains TARDY: cannot create tardy model for: "SER A 29 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE A 462 " (corrupted residue). Skipping it. outliers start: 16 outliers final: 15 residues processed: 142 average time/residue: 0.9640 time to fit residues: 147.1748 Evaluate side-chains 146 residues out of total 788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 131 time to evaluate : 0.933 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 11 residues processed: 4 average time/residue: 0.8080 time to fit residues: 4.5722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 34 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 75 optimal weight: 0.0980 chunk 79 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 84 optimal weight: 0.0040 chunk 51 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 58 optimal weight: 6.9990 overall best weight: 1.4198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 54 ASN N 77 ASN ** N 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8756 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 : 0.005 0.037 8203 Z= 0.291 Angle : 1.079 16.046 11363 Z= 0.418 Chirality : 0.041 0.163 1137 Planarity : 0.004 0.035 1243 Dihedral : 23.941 170.085 2112 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 41.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer Outliers : 1.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.28), residues: 888 helix: 2.23 (0.26), residues: 382 sheet: 0.58 (0.36), residues: 201 loop : -0.96 (0.33), residues: 305 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 133 time to evaluate : 0.865 Fit side-chains TARDY: cannot create tardy model for: "SER A 29 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE A 462 " (corrupted residue). Skipping it. outliers start: 14 outliers final: 13 residues processed: 144 average time/residue: 0.9537 time to fit residues: 147.6699 Evaluate side-chains 146 residues out of total 788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 133 time to evaluate : 0.829 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 11 residues processed: 2 average time/residue: 0.1234 time to fit residues: 1.4810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 88 optimal weight: 0.9990 chunk 81 optimal weight: 0.4980 chunk 70 optimal weight: 4.9990 chunk 7 optimal weight: 1.9990 chunk 54 optimal weight: 0.9980 chunk 43 optimal weight: 0.8980 chunk 56 optimal weight: 1.9990 chunk 75 optimal weight: 0.0030 chunk 21 optimal weight: 0.9980 chunk 65 optimal weight: 0.2980 chunk 10 optimal weight: 0.7980 overall best weight: 0.4990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 54 ASN N 77 ASN ** N 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8750 moved from start: 0.1182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 8203 Z= 0.195 Angle : 1.061 15.858 11363 Z= 0.411 Chirality : 0.039 0.163 1137 Planarity : 0.004 0.034 1243 Dihedral : 23.854 170.202 2112 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 41.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer Outliers : 2.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.28), residues: 888 helix: 2.28 (0.26), residues: 381 sheet: 0.57 (0.36), residues: 201 loop : -0.92 (0.33), residues: 306 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 130 time to evaluate : 0.906 Fit side-chains TARDY: cannot create tardy model for: "SER A 29 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE A 462 " (corrupted residue). Skipping it. outliers start: 15 outliers final: 14 residues processed: 141 average time/residue: 0.9966 time to fit residues: 151.6049 Evaluate side-chains 144 residues out of total 788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 130 time to evaluate : 0.812 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 11 residues processed: 3 average time/residue: 0.1332 time to fit residues: 1.6778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 19 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 chunk 80 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 54 ASN N 77 ASN ** N 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.138801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.100192 restraints weight = 36724.358| |-----------------------------------------------------------------------------| r_work (start): 0.3028 rms_B_bonded: 3.40 r_work: 0.3001 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2978 rms_B_bonded: 3.02 restraints_weight: 0.2500 r_work: 0.2956 rms_B_bonded: 3.14 restraints_weight: 0.1250 r_work: 0.2932 rms_B_bonded: 3.37 restraints_weight: 0.0625 r_work: 0.2907 rms_B_bonded: 3.69 restraints_weight: 0.0312 r_work: 0.2880 rms_B_bonded: 4.11 restraints_weight: 0.0156 r_work: 0.2851 rms_B_bonded: 4.62 restraints_weight: 0.0078 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8830 moved from start: 0.1182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.037 8203 Z= 0.290 Angle : 1.068 15.795 11363 Z= 0.414 Chirality : 0.042 0.163 1137 Planarity : 0.004 0.035 1243 Dihedral : 23.881 170.125 2112 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 41.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer Outliers : 1.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.28), residues: 888 helix: 2.27 (0.26), residues: 381 sheet: 0.57 (0.36), residues: 201 loop : -0.95 (0.33), residues: 306 =============================================================================== Job complete usr+sys time: 2998.25 seconds wall clock time: 54 minutes 12.83 seconds (3252.83 seconds total)