Mon 24 Dec 07:26:56 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2ii1-4.0-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2ii1-4.0-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2ii1-4.0-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2ii1-4.0-parrot-noncs Accepted label: fp=FP Accepted label: sigfp=SIGFP Accepted label: phibest=hltofom.Phi_fom.phi Accepted label: fom=hltofom.Phi_fom.fom mtz labels taken: FP SIGFP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Parameter file /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2ii1-4.0-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2ii1-4.0-parrot-noncs ############### You are running ARP/wARP 8.0 ############### ============================================================ Please cite at least one of the publications below for the ARP/wARP application you are using: Lamzin VS, Wilson KS. (1993) Automated refinement of protein models. Acta Crystallogr D Biol Crystallogr. 49, 129-147 Morris RJ, Perrakis A. Lamzin VS. (2003) ARP/wARP and automatic interpretation of protein electron density maps. In Methods Enzymol. (Carter, C.W. & Sweet, R.M. eds.) 374, 229-244 Langer GG, Hazledine S, Wiegels T, Carolan C, Lamzin VS. (2013) Visual automated macromolecular model building. Acta Crystallogr D Biol Crystallogr. 69, 635-641 Use of Refmac is an essential part of model building with ARP/wARP. Please acknowledge the use of Refmac by citing the following publication: Murshudov GN, Skubak P, Lebedev AA, Pannu NS, Steiner RA, Nicholls RA, Winn MD, Long F, Vagin AA. (2011) REFMAC5 for the refinement of macromolecular crystal structures. Acta Crystallogr D Biol Crystallogr. 67, 355-367 ============================================================ Mon 24 Dec 07:27:00 GMT 2018 You are running ARP/wARP version 8.0 Entering warp_tracing.sh from COMMAND_LINE_SUBMISSION The working directory: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2ii1-4.0-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2ii1-4.0-parrot-noncs/arp_warp_classic.par ARP/wARP will run in subdirectory: temp_tracing Checking the estimated solvent content Computed solvent content is outside allowed range. Target number of residues/nucleotides is changed to 727 and 0 Target number of residues in the AU: 727 Target solvent content: 0.6456 Checking the provided sequence file Detected sequence length: 301 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 1204 Adjusted target solvent content: 0.41 Input MTZ file: 2ii1-4.0-parrot-noncs.mtz.cad Column labels for model refinement: FP SIGFP Column labels to obtain initial map: FP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Space group number: 1 Cell parameters: 43.759 69.605 94.984 73.954 88.905 86.625 Input sequence file: 2ii1-4.0-parrot-noncs.fasta_lf Building free atoms model in initial map for 9632 target number of atoms Had to go as low as 0.65 sigma, to complete atoms search. ARP/wARP will be iterated with REFMAC5 50 refinement / model update cycles will be run in total. Atoms will be removed below 1.0 sigma in 2mFoDFc map and added above 3.2 sigma in mFoDFc map. Refmac Refinement Parameters 3 REFMAC cycle(s) with 1.0 1.0 fractional shifts damping in each cycle. Conditional restraints will be used Weight for restraints is set to AUTO Solvent mask correction will be used Anisotropic scaling with no bulk solvent correction Model Building Parameters Main chain tracing will take place every 5 refinement / model update cycles. Side chain docking will be performed from autobuilding cycle number 1 NCS extension will be performed at every building cycle. NCS restraints will be applied at each refinement cycle. Loops will be built when appropriate and at the last cycle Resolution range: 91.283 4.000 Wilson plot Bfac: 75.38 8241 reflections ( 91.02 % complete ) and 0 restraints for refining 10692 atoms. Observations/parameters ratio is 0.19 ------------------------------------------------------ Starting model: R = 0.3397 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3194 (Rfree = 0.000) for 10692 atoms. Found 50 (50 requested) and removed 167 (25 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.64 4.11 Search for helices and strands: 0 residues in 0 chains, 10667 seeds are put forward NCS extension: 0 residues added, 10667 seeds are put forward Round 1: 198 peptides, 46 chains. Longest chain 7 peptides. Score 0.197 Round 2: 246 peptides, 52 chains. Longest chain 8 peptides. Score 0.241 Round 3: 277 peptides, 56 chains. Longest chain 8 peptides. Score 0.267 Round 4: 270 peptides, 55 chains. Longest chain 8 peptides. Score 0.262 Round 5: 278 peptides, 53 chains. Longest chain 11 peptides. Score 0.291 Taking the results from Round 5 Chains 53, Residues 225, Estimated correctness of the model 0.0 % 3 chains (17 residues) have been docked in sequence ------------------------------------------------------ 8241 reflections ( 91.02 % complete ) and 22100 restraints for refining 8695 atoms. 21218 conditional restraints added. Observations/parameters ratio is 0.24 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2604 (Rfree = 0.000) for 8695 atoms. Found 28 (41 requested) and removed 72 (20 requested) atoms. Failed to save intermediate PDB Cycle 2: After refmac, R = 0.2462 (Rfree = 0.000) for 8554 atoms. Found 41 (41 requested) and removed 66 (20 requested) atoms. Cycle 3: After refmac, R = 0.1823 (Rfree = 0.000) for 8485 atoms. Found 10 (40 requested) and removed 42 (20 requested) atoms. Cycle 4: After refmac, R = 0.1733 (Rfree = 0.000) for 8423 atoms. Found 6 (40 requested) and removed 33 (20 requested) atoms. Cycle 5: After refmac, R = 0.1719 (Rfree = 0.000) for 8374 atoms. Found 8 (39 requested) and removed 35 (19 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.62 4.09 Search for helices and strands: 0 residues in 0 chains, 8490 seeds are put forward NCS extension: 10 residues added (0 deleted due to clashes), 8500 seeds are put forward Round 1: 257 peptides, 58 chains. Longest chain 6 peptides. Score 0.215 Round 2: 330 peptides, 67 chains. Longest chain 11 peptides. Score 0.278 Round 3: 359 peptides, 71 chains. Longest chain 11 peptides. Score 0.298 Round 4: 371 peptides, 74 chains. Longest chain 11 peptides. Score 0.296 Round 5: 364 peptides, 69 chains. Longest chain 12 peptides. Score 0.319 Taking the results from Round 5 Chains 69, Residues 295, Estimated correctness of the model 0.0 % 3 chains (12 residues) have been docked in sequence ------------------------------------------------------ 8241 reflections ( 91.02 % complete ) and 19125 restraints for refining 7844 atoms. 17981 conditional restraints added. Observations/parameters ratio is 0.26 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2284 (Rfree = 0.000) for 7844 atoms. Found 37 (37 requested) and removed 65 (18 requested) atoms. Cycle 7: After refmac, R = 0.2081 (Rfree = 0.000) for 7775 atoms. Found 37 (37 requested) and removed 55 (18 requested) atoms. Cycle 8: After refmac, R = 0.1982 (Rfree = 0.000) for 7723 atoms. Found 29 (36 requested) and removed 57 (18 requested) atoms. Cycle 9: After refmac, R = 0.1976 (Rfree = 0.000) for 7669 atoms. Found 36 (36 requested) and removed 39 (18 requested) atoms. Cycle 10: After refmac, R = 0.1954 (Rfree = 0.000) for 7648 atoms. Found 36 (36 requested) and removed 34 (18 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.64 4.11 Search for helices and strands: 0 residues in 0 chains, 7803 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 7819 seeds are put forward Round 1: 296 peptides, 66 chains. Longest chain 8 peptides. Score 0.226 Round 2: 353 peptides, 69 chains. Longest chain 16 peptides. Score 0.302 Round 3: 356 peptides, 65 chains. Longest chain 20 peptides. Score 0.334 Round 4: 340 peptides, 61 chains. Longest chain 17 peptides. Score 0.336 Round 5: 354 peptides, 64 chains. Longest chain 24 peptides. Score 0.338 Taking the results from Round 5 Chains 66, Residues 290, Estimated correctness of the model 0.0 % 5 chains (30 residues) have been docked in sequence ------------------------------------------------------ 8241 reflections ( 91.02 % complete ) and 18047 restraints for refining 7636 atoms. 16871 conditional restraints added. Observations/parameters ratio is 0.27 ------------------------------------------------------ Cycle 11: After refmac, R = 0.1970 (Rfree = 0.000) for 7636 atoms. Found 36 (36 requested) and removed 60 (18 requested) atoms. Cycle 12: After refmac, R = 0.1937 (Rfree = 0.000) for 7573 atoms. Found 36 (36 requested) and removed 42 (18 requested) atoms. Cycle 13: After refmac, R = 0.1893 (Rfree = 0.000) for 7543 atoms. Found 35 (35 requested) and removed 39 (17 requested) atoms. Cycle 14: After refmac, R = 0.1806 (Rfree = 0.000) for 7528 atoms. Found 29 (35 requested) and removed 34 (17 requested) atoms. Cycle 15: After refmac, R = 0.1462 (Rfree = 0.000) for 7502 atoms. Found 12 (35 requested) and removed 24 (17 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.59 4.05 Search for helices and strands: 0 residues in 0 chains, 7679 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 7695 seeds are put forward Round 1: 350 peptides, 75 chains. Longest chain 9 peptides. Score 0.255 Round 2: 369 peptides, 71 chains. Longest chain 13 peptides. Score 0.314 Round 3: 377 peptides, 70 chains. Longest chain 12 peptides. Score 0.333 Round 4: 385 peptides, 68 chains. Longest chain 14 peptides. Score 0.359 Round 5: 365 peptides, 63 chains. Longest chain 10 peptides. Score 0.362 Taking the results from Round 5 Chains 63, Residues 302, Estimated correctness of the model 0.0 % 6 chains (33 residues) have been docked in sequence ------------------------------------------------------ 8241 reflections ( 91.02 % complete ) and 18595 restraints for refining 7869 atoms. 17369 conditional restraints added. Observations/parameters ratio is 0.26 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1989 (Rfree = 0.000) for 7869 atoms. Found 37 (37 requested) and removed 83 (18 requested) atoms. Cycle 17: After refmac, R = 0.1849 (Rfree = 0.000) for 7774 atoms. Found 36 (37 requested) and removed 49 (18 requested) atoms. Cycle 18: After refmac, R = 0.1443 (Rfree = 0.000) for 7741 atoms. Found 15 (36 requested) and removed 31 (18 requested) atoms. Cycle 19: After refmac, R = 0.1569 (Rfree = 0.000) for 7712 atoms. Found 23 (36 requested) and removed 34 (18 requested) atoms. Cycle 20: After refmac, R = 0.1361 (Rfree = 0.000) for 7694 atoms. Found 7 (36 requested) and removed 25 (18 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.57 4.03 Search for helices and strands: 0 residues in 0 chains, 7845 seeds are put forward NCS extension: 11 residues added (1 deleted due to clashes), 7856 seeds are put forward Round 1: 343 peptides, 72 chains. Longest chain 9 peptides. Score 0.264 Round 2: 363 peptides, 67 chains. Longest chain 13 peptides. Score 0.332 Round 3: 355 peptides, 62 chains. Longest chain 15 peptides. Score 0.353 Round 4: 366 peptides, 61 chains. Longest chain 17 peptides. Score 0.377 Round 5: 344 peptides, 64 chains. Longest chain 13 peptides. Score 0.322 Taking the results from Round 4 Chains 61, Residues 305, Estimated correctness of the model 0.0 % 8 chains (38 residues) have been docked in sequence ------------------------------------------------------ 8241 reflections ( 91.02 % complete ) and 18544 restraints for refining 7964 atoms. 17298 conditional restraints added. Observations/parameters ratio is 0.26 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1706 (Rfree = 0.000) for 7964 atoms. Found 30 (37 requested) and removed 55 (18 requested) atoms. Cycle 22: After refmac, R = 0.1568 (Rfree = 0.000) for 7903 atoms. Found 29 (37 requested) and removed 53 (18 requested) atoms. Cycle 23: After refmac, R = 0.1581 (Rfree = 0.000) for 7861 atoms. Found 37 (37 requested) and removed 32 (18 requested) atoms. Cycle 24: After refmac, R = 0.1535 (Rfree = 0.000) for 7846 atoms. Found 37 (37 requested) and removed 28 (18 requested) atoms. Cycle 25: After refmac, R = 0.1104 (Rfree = 0.000) for 7844 atoms. Found 10 (37 requested) and removed 21 (18 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.57 4.03 Search for helices and strands: 0 residues in 0 chains, 8010 seeds are put forward NCS extension: 21 residues added (1 deleted due to clashes), 8031 seeds are put forward Round 1: 320 peptides, 71 chains. Longest chain 9 peptides. Score 0.232 Round 2: 374 peptides, 71 chains. Longest chain 18 peptides. Score 0.322 Round 3: 382 peptides, 71 chains. Longest chain 14 peptides. Score 0.334 Round 4: 366 peptides, 67 chains. Longest chain 15 peptides. Score 0.336 Round 5: 391 peptides, 70 chains. Longest chain 18 peptides. Score 0.355 Taking the results from Round 5 Chains 71, Residues 321, Estimated correctness of the model 0.0 % 8 chains (34 residues) have been docked in sequence ------------------------------------------------------ 8241 reflections ( 91.02 % complete ) and 19187 restraints for refining 8141 atoms. 17914 conditional restraints added. Observations/parameters ratio is 0.25 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1649 (Rfree = 0.000) for 8141 atoms. Found 38 (38 requested) and removed 48 (19 requested) atoms. Cycle 27: After refmac, R = 0.1591 (Rfree = 0.000) for 8090 atoms. Found 38 (38 requested) and removed 44 (19 requested) atoms. Failed to save intermediate PDB Cycle 28: After refmac, R = 0.1603 (Rfree = 0.000) for 8056 atoms. Found 38 (38 requested) and removed 34 (19 requested) atoms. Cycle 29: After refmac, R = 0.1201 (Rfree = 0.000) for 8043 atoms. Found 10 (38 requested) and removed 28 (19 requested) atoms. Cycle 30: After refmac, R = 0.1119 (Rfree = 0.000) for 8020 atoms. Found 5 (38 requested) and removed 20 (19 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.59 4.05 Search for helices and strands: 0 residues in 0 chains, 8173 seeds are put forward NCS extension: 12 residues added (1 deleted due to clashes), 8185 seeds are put forward Round 1: 278 peptides, 61 chains. Longest chain 15 peptides. Score 0.231 Round 2: 311 peptides, 59 chains. Longest chain 21 peptides. Score 0.303 Round 3: 317 peptides, 59 chains. Longest chain 16 peptides. Score 0.313 Round 4: 312 peptides, 62 chains. Longest chain 15 peptides. Score 0.283 Round 5: 336 peptides, 63 chains. Longest chain 13 peptides. Score 0.316 Taking the results from Round 5 Chains 63, Residues 273, Estimated correctness of the model 0.0 % 6 chains (21 residues) have been docked in sequence ------------------------------------------------------ 8241 reflections ( 91.02 % complete ) and 20105 restraints for refining 8298 atoms. 19038 conditional restraints added. Observations/parameters ratio is 0.25 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1754 (Rfree = 0.000) for 8298 atoms. Found 39 (39 requested) and removed 55 (19 requested) atoms. Cycle 32: After refmac, R = 0.1806 (Rfree = 0.000) for 8258 atoms. Found 39 (39 requested) and removed 51 (19 requested) atoms. Cycle 33: After refmac, R = 0.1768 (Rfree = 0.000) for 8229 atoms. Found 39 (39 requested) and removed 45 (19 requested) atoms. Cycle 34: After refmac, R = 0.1724 (Rfree = 0.000) for 8210 atoms. Found 39 (39 requested) and removed 39 (19 requested) atoms. Cycle 35: After refmac, R = 0.1287 (Rfree = 0.000) for 8197 atoms. Found 16 (39 requested) and removed 26 (19 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.62 4.09 Search for helices and strands: 0 residues in 0 chains, 8334 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 8351 seeds are put forward Round 1: 278 peptides, 62 chains. Longest chain 8 peptides. Score 0.223 Round 2: 329 peptides, 68 chains. Longest chain 8 peptides. Score 0.269 Round 3: 338 peptides, 66 chains. Longest chain 10 peptides. Score 0.298 Round 4: 352 peptides, 68 chains. Longest chain 11 peptides. Score 0.307 Round 5: 335 peptides, 64 chains. Longest chain 10 peptides. Score 0.307 Taking the results from Round 5 Chains 64, Residues 271, Estimated correctness of the model 0.0 % 4 chains (17 residues) have been docked in sequence ------------------------------------------------------ 8241 reflections ( 91.02 % complete ) and 20239 restraints for refining 8286 atoms. 19181 conditional restraints added. Observations/parameters ratio is 0.25 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1723 (Rfree = 0.000) for 8286 atoms. Found 39 (39 requested) and removed 63 (19 requested) atoms. Cycle 37: After refmac, R = 0.1606 (Rfree = 0.000) for 8240 atoms. Found 39 (39 requested) and removed 49 (19 requested) atoms. Cycle 38: After refmac, R = 0.1598 (Rfree = 0.000) for 8214 atoms. Found 39 (39 requested) and removed 42 (19 requested) atoms. Cycle 39: After refmac, R = 0.1550 (Rfree = 0.000) for 8194 atoms. Found 39 (39 requested) and removed 25 (19 requested) atoms. Cycle 40: After refmac, R = 0.1438 (Rfree = 0.000) for 8191 atoms. Found 38 (38 requested) and removed 28 (19 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.62 4.09 Search for helices and strands: 0 residues in 0 chains, 8381 seeds are put forward NCS extension: 12 residues added (0 deleted due to clashes), 8393 seeds are put forward Round 1: 260 peptides, 58 chains. Longest chain 7 peptides. Score 0.221 Round 2: 304 peptides, 61 chains. Longest chain 12 peptides. Score 0.277 Round 3: 308 peptides, 57 chains. Longest chain 11 peptides. Score 0.312 Round 4: 327 peptides, 63 chains. Longest chain 11 peptides. Score 0.301 Round 5: 313 peptides, 55 chains. Longest chain 15 peptides. Score 0.335 Taking the results from Round 5 Chains 55, Residues 258, Estimated correctness of the model 0.0 % 4 chains (16 residues) have been docked in sequence ------------------------------------------------------ 8241 reflections ( 91.02 % complete ) and 20438 restraints for refining 8344 atoms. 19421 conditional restraints added. Observations/parameters ratio is 0.25 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1560 (Rfree = 0.000) for 8344 atoms. Found 39 (39 requested) and removed 58 (19 requested) atoms. Cycle 42: After refmac, R = 0.1500 (Rfree = 0.000) for 8296 atoms. Found 39 (39 requested) and removed 40 (19 requested) atoms. Cycle 43: After refmac, R = 0.1524 (Rfree = 0.000) for 8283 atoms. Found 39 (39 requested) and removed 33 (19 requested) atoms. Cycle 44: After refmac, R = 0.1438 (Rfree = 0.000) for 8271 atoms. Found 39 (39 requested) and removed 35 (19 requested) atoms. Failed to save intermediate PDB Cycle 45: After refmac, R = 0.1474 (Rfree = 0.000) for 8264 atoms. Found 39 (39 requested) and removed 41 (19 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.56 4.02 Search for helices and strands: 0 residues in 0 chains, 8412 seeds are put forward NCS extension: 22 residues added (1 deleted due to clashes), 8434 seeds are put forward Round 1: 228 peptides, 52 chains. Longest chain 7 peptides. Score 0.207 Round 2: 246 peptides, 48 chains. Longest chain 13 peptides. Score 0.273 Round 3: 233 peptides, 48 chains. Longest chain 8 peptides. Score 0.249 Round 4: 240 peptides, 46 chains. Longest chain 8 peptides. Score 0.278 Round 5: 231 peptides, 42 chains. Longest chain 12 peptides. Score 0.293 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 42, Residues 189, Estimated correctness of the model 0.0 % 4 chains (14 residues) have been docked in sequence Sequence coverage is 7 % Consider running further cycles of model building using 2ii1-4_warpNtrace.pdb as input Building loops using Loopy2018 42 chains (189 residues) following loop building 4 chains (14 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 8241 reflections ( 91.02 % complete ) and 20703 restraints for refining 8275 atoms. 19954 conditional restraints added. Observations/parameters ratio is 0.25 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1682 (Rfree = 0.000) for 8275 atoms. Found 0 (39 requested) and removed 19 (19 requested) atoms. Cycle 47: After refmac, R = 0.1644 (Rfree = 0.000) for 8235 atoms. Found 0 (39 requested) and removed 19 (19 requested) atoms. Cycle 48: After refmac, R = 0.1613 (Rfree = 0.000) for 8201 atoms. Found 0 (39 requested) and removed 19 (19 requested) atoms. Cycle 49: After refmac, R = 0.1293 (Rfree = 0.000) for 8172 atoms. TimeTaking 81.42