Mon 24 Dec 07:34:55 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 2afb-3.4-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2afb-3.4-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2afb-3.4-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2afb-3.4-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/2afb-3.4-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2afb-3.4-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 07:35:00 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/2afb-3.4-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2afb-3.4-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 506 and 0 Target number of residues in the AU: 506 Target solvent content: 0.6266 Checking the provided sequence file Detected sequence length: 351 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 702 Adjusted target solvent content: 0.48 Input MTZ file: 2afb-3.4-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: 155 Cell parameters: 120.993 120.993 260.300 90.000 90.000 120.000 Input sequence file: 2afb-3.4-parrot-noncs.fasta_lf Building free atoms model in initial map for 5616 target number of atoms Had to go as low as 0.70 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: 97.203 3.400 Wilson plot Bfac: 64.64 10354 reflections ( 99.53 % complete ) and 0 restraints for refining 6248 atoms. Observations/parameters ratio is 0.41 ------------------------------------------------------ Starting model: R = 0.3222 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3398 (Rfree = 0.000) for 6248 atoms. Found 44 (47 requested) and removed 68 (23 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.37 3.46 Search for helices and strands: 0 residues in 0 chains, 6342 seeds are put forward NCS extension: 0 residues added, 6342 seeds are put forward Round 1: 240 peptides, 46 chains. Longest chain 14 peptides. Score 0.314 Round 2: 310 peptides, 50 chains. Longest chain 18 peptides. Score 0.434 Round 3: 341 peptides, 51 chains. Longest chain 21 peptides. Score 0.488 Round 4: 363 peptides, 49 chains. Longest chain 21 peptides. Score 0.546 Round 5: 377 peptides, 49 chains. Longest chain 22 peptides. Score 0.571 Taking the results from Round 5 Chains 54, Residues 328, Estimated correctness of the model 18.9 % 7 chains (51 residues) have been docked in sequence ------------------------------------------------------ 10354 reflections ( 99.53 % complete ) and 11166 restraints for refining 5106 atoms. 9760 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2875 (Rfree = 0.000) for 5106 atoms. Found 26 (38 requested) and removed 43 (19 requested) atoms. Cycle 2: After refmac, R = 0.2715 (Rfree = 0.000) for 5008 atoms. Found 37 (38 requested) and removed 64 (19 requested) atoms. Cycle 3: After refmac, R = 0.2586 (Rfree = 0.000) for 4947 atoms. Found 20 (37 requested) and removed 34 (18 requested) atoms. Cycle 4: After refmac, R = 0.2286 (Rfree = 0.000) for 4903 atoms. Found 15 (37 requested) and removed 22 (18 requested) atoms. Cycle 5: After refmac, R = 0.2245 (Rfree = 0.000) for 4881 atoms. Found 9 (36 requested) and removed 25 (18 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.37 3.46 Search for helices and strands: 0 residues in 0 chains, 5048 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 5064 seeds are put forward Round 1: 361 peptides, 56 chains. Longest chain 20 peptides. Score 0.484 Round 2: 416 peptides, 53 chains. Longest chain 19 peptides. Score 0.606 Round 3: 414 peptides, 46 chains. Longest chain 29 peptides. Score 0.651 Round 4: 409 peptides, 51 chains. Longest chain 23 peptides. Score 0.609 Round 5: 425 peptides, 51 chains. Longest chain 25 peptides. Score 0.634 Taking the results from Round 3 Chains 48, Residues 368, Estimated correctness of the model 44.4 % 3 chains (30 residues) have been docked in sequence ------------------------------------------------------ 10354 reflections ( 99.53 % complete ) and 11052 restraints for refining 5047 atoms. 9515 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2631 (Rfree = 0.000) for 5047 atoms. Found 37 (38 requested) and removed 56 (19 requested) atoms. Cycle 7: After refmac, R = 0.2433 (Rfree = 0.000) for 4991 atoms. Found 18 (37 requested) and removed 28 (18 requested) atoms. Cycle 8: After refmac, R = 0.2322 (Rfree = 0.000) for 4954 atoms. Found 19 (37 requested) and removed 31 (18 requested) atoms. Cycle 9: After refmac, R = 0.2049 (Rfree = 0.000) for 4917 atoms. Found 12 (37 requested) and removed 19 (18 requested) atoms. Cycle 10: After refmac, R = 0.2113 (Rfree = 0.000) for 4896 atoms. Found 8 (37 requested) and removed 20 (18 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.25 3.34 Search for helices and strands: 0 residues in 0 chains, 5087 seeds are put forward NCS extension: 31 residues added (4 deleted due to clashes), 5118 seeds are put forward Round 1: 373 peptides, 57 chains. Longest chain 23 peptides. Score 0.499 Round 2: 404 peptides, 51 chains. Longest chain 33 peptides. Score 0.601 Round 3: 422 peptides, 52 chains. Longest chain 40 peptides. Score 0.622 Round 4: 420 peptides, 49 chains. Longest chain 27 peptides. Score 0.640 Round 5: 386 peptides, 46 chains. Longest chain 33 peptides. Score 0.608 Taking the results from Round 4 Chains 53, Residues 371, Estimated correctness of the model 41.2 % 9 chains (56 residues) have been docked in sequence ------------------------------------------------------ 10354 reflections ( 99.53 % complete ) and 11008 restraints for refining 5103 atoms. 9402 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2523 (Rfree = 0.000) for 5103 atoms. Found 25 (38 requested) and removed 56 (19 requested) atoms. Cycle 12: After refmac, R = 0.2536 (Rfree = 0.000) for 5034 atoms. Found 31 (38 requested) and removed 31 (19 requested) atoms. Cycle 13: After refmac, R = 0.2489 (Rfree = 0.000) for 5022 atoms. Found 15 (38 requested) and removed 28 (19 requested) atoms. Failed to save intermediate PDB Cycle 14: After refmac, R = 0.2446 (Rfree = 0.000) for 4992 atoms. Found 24 (37 requested) and removed 26 (18 requested) atoms. Cycle 15: After refmac, R = 0.2393 (Rfree = 0.000) for 4976 atoms. Found 26 (37 requested) and removed 26 (18 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.28 3.37 Search for helices and strands: 0 residues in 0 chains, 5181 seeds are put forward NCS extension: 32 residues added (3 deleted due to clashes), 5213 seeds are put forward Round 1: 349 peptides, 55 chains. Longest chain 13 peptides. Score 0.469 Round 2: 385 peptides, 53 chains. Longest chain 21 peptides. Score 0.553 Round 3: 405 peptides, 52 chains. Longest chain 23 peptides. Score 0.595 Round 4: 402 peptides, 51 chains. Longest chain 28 peptides. Score 0.598 Round 5: 414 peptides, 53 chains. Longest chain 27 peptides. Score 0.602 Taking the results from Round 5 Chains 56, Residues 361, Estimated correctness of the model 29.3 % 7 chains (43 residues) have been docked in sequence ------------------------------------------------------ 10354 reflections ( 99.53 % complete ) and 11146 restraints for refining 5106 atoms. 9645 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2560 (Rfree = 0.000) for 5106 atoms. Found 33 (38 requested) and removed 30 (19 requested) atoms. Cycle 17: After refmac, R = 0.2469 (Rfree = 0.000) for 5082 atoms. Found 38 (38 requested) and removed 26 (19 requested) atoms. Cycle 18: After refmac, R = 0.2392 (Rfree = 0.000) for 5058 atoms. Found 29 (38 requested) and removed 31 (19 requested) atoms. Cycle 19: After refmac, R = 0.2297 (Rfree = 0.000) for 5039 atoms. Found 35 (38 requested) and removed 23 (19 requested) atoms. Cycle 20: After refmac, R = 0.2277 (Rfree = 0.000) for 5030 atoms. Found 33 (38 requested) and removed 25 (19 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.27 3.36 Search for helices and strands: 0 residues in 0 chains, 5253 seeds are put forward NCS extension: 19 residues added (1 deleted due to clashes), 5272 seeds are put forward Round 1: 344 peptides, 62 chains. Longest chain 14 peptides. Score 0.396 Round 2: 376 peptides, 53 chains. Longest chain 29 peptides. Score 0.537 Round 3: 368 peptides, 49 chains. Longest chain 27 peptides. Score 0.555 Round 4: 388 peptides, 53 chains. Longest chain 19 peptides. Score 0.559 Round 5: 416 peptides, 56 chains. Longest chain 32 peptides. Score 0.584 Taking the results from Round 5 Chains 57, Residues 360, Estimated correctness of the model 23.4 % 5 chains (31 residues) have been docked in sequence ------------------------------------------------------ 10354 reflections ( 99.53 % complete ) and 11252 restraints for refining 5106 atoms. 9786 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2480 (Rfree = 0.000) for 5106 atoms. Found 30 (38 requested) and removed 25 (19 requested) atoms. Cycle 22: After refmac, R = 0.2209 (Rfree = 0.000) for 5081 atoms. Found 11 (38 requested) and removed 23 (19 requested) atoms. Cycle 23: After refmac, R = 0.2060 (Rfree = 0.000) for 5055 atoms. Found 14 (38 requested) and removed 22 (19 requested) atoms. Cycle 24: After refmac, R = 0.1984 (Rfree = 0.000) for 5038 atoms. Found 7 (38 requested) and removed 21 (19 requested) atoms. Cycle 25: After refmac, R = 0.1965 (Rfree = 0.000) for 5014 atoms. Found 10 (37 requested) and removed 18 (18 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.28 3.37 Search for helices and strands: 0 residues in 0 chains, 5185 seeds are put forward NCS extension: 20 residues added (0 deleted due to clashes), 5205 seeds are put forward Round 1: 344 peptides, 53 chains. Longest chain 15 peptides. Score 0.477 Round 2: 394 peptides, 49 chains. Longest chain 23 peptides. Score 0.599 Round 3: 385 peptides, 50 chains. Longest chain 17 peptides. Score 0.577 Round 4: 385 peptides, 50 chains. Longest chain 24 peptides. Score 0.577 Round 5: 395 peptides, 52 chains. Longest chain 21 peptides. Score 0.578 Taking the results from Round 2 Chains 50, Residues 345, Estimated correctness of the model 28.3 % 6 chains (63 residues) have been docked in sequence ------------------------------------------------------ 10354 reflections ( 99.53 % complete ) and 10926 restraints for refining 5105 atoms. 9360 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2398 (Rfree = 0.000) for 5105 atoms. Found 28 (38 requested) and removed 23 (19 requested) atoms. Cycle 27: After refmac, R = 0.2225 (Rfree = 0.000) for 5092 atoms. Found 12 (38 requested) and removed 24 (19 requested) atoms. Cycle 28: After refmac, R = 0.2159 (Rfree = 0.000) for 5070 atoms. Found 18 (38 requested) and removed 22 (19 requested) atoms. Cycle 29: After refmac, R = 0.2062 (Rfree = 0.000) for 5058 atoms. Found 12 (38 requested) and removed 20 (19 requested) atoms. Cycle 30: After refmac, R = 0.2052 (Rfree = 0.000) for 5044 atoms. Found 11 (38 requested) and removed 20 (19 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.31 3.40 Search for helices and strands: 0 residues in 0 chains, 5209 seeds are put forward NCS extension: 32 residues added (0 deleted due to clashes), 5241 seeds are put forward Round 1: 333 peptides, 53 chains. Longest chain 15 peptides. Score 0.454 Round 2: 369 peptides, 48 chains. Longest chain 21 peptides. Score 0.565 Round 3: 384 peptides, 51 chains. Longest chain 23 peptides. Score 0.567 Round 4: 376 peptides, 46 chains. Longest chain 23 peptides. Score 0.592 Round 5: 387 peptides, 44 chains. Longest chain 28 peptides. Score 0.624 Taking the results from Round 5 Chains 44, Residues 343, Estimated correctness of the model 36.3 % 2 chains (29 residues) have been docked in sequence ------------------------------------------------------ 10354 reflections ( 99.53 % complete ) and 11361 restraints for refining 5105 atoms. 9940 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2813 (Rfree = 0.000) for 5105 atoms. Found 38 (38 requested) and removed 26 (19 requested) atoms. Cycle 32: After refmac, R = 0.2482 (Rfree = 0.000) for 5098 atoms. Found 38 (38 requested) and removed 28 (19 requested) atoms. Cycle 33: After refmac, R = 0.2088 (Rfree = 0.000) for 5089 atoms. Found 19 (38 requested) and removed 24 (19 requested) atoms. Cycle 34: After refmac, R = 0.1938 (Rfree = 0.000) for 5068 atoms. Found 6 (38 requested) and removed 19 (19 requested) atoms. Cycle 35: After refmac, R = 0.2028 (Rfree = 0.000) for 5045 atoms. Found 20 (38 requested) and removed 19 (19 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.28 3.37 Search for helices and strands: 0 residues in 0 chains, 5228 seeds are put forward NCS extension: 44 residues added (2 deleted due to clashes), 5272 seeds are put forward Round 1: 301 peptides, 52 chains. Longest chain 15 peptides. Score 0.396 Round 2: 343 peptides, 51 chains. Longest chain 19 peptides. Score 0.492 Round 3: 343 peptides, 45 chains. Longest chain 24 peptides. Score 0.542 Round 4: 373 peptides, 48 chains. Longest chain 20 peptides. Score 0.572 Round 5: 362 peptides, 46 chains. Longest chain 22 peptides. Score 0.568 Taking the results from Round 4 Chains 49, Residues 325, Estimated correctness of the model 19.3 % 6 chains (47 residues) have been docked in sequence ------------------------------------------------------ 10354 reflections ( 99.53 % complete ) and 11159 restraints for refining 5106 atoms. 9760 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2436 (Rfree = 0.000) for 5106 atoms. Found 33 (38 requested) and removed 31 (19 requested) atoms. Cycle 37: After refmac, R = 0.2451 (Rfree = 0.000) for 5086 atoms. Found 38 (38 requested) and removed 24 (19 requested) atoms. Cycle 38: After refmac, R = 0.2301 (Rfree = 0.000) for 5089 atoms. Found 38 (38 requested) and removed 24 (19 requested) atoms. Cycle 39: After refmac, R = 0.2186 (Rfree = 0.000) for 5088 atoms. Found 30 (38 requested) and removed 23 (19 requested) atoms. Cycle 40: After refmac, R = 0.2135 (Rfree = 0.000) for 5086 atoms. Found 30 (38 requested) and removed 19 (19 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.23 3.32 Search for helices and strands: 0 residues in 0 chains, 5246 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 5265 seeds are put forward Round 1: 276 peptides, 50 chains. Longest chain 13 peptides. Score 0.359 Round 2: 319 peptides, 49 chains. Longest chain 19 peptides. Score 0.461 Round 3: 327 peptides, 52 chains. Longest chain 21 peptides. Score 0.451 Round 4: 330 peptides, 45 chains. Longest chain 22 peptides. Score 0.518 Round 5: 316 peptides, 48 chains. Longest chain 16 peptides. Score 0.464 Taking the results from Round 4 Chains 46, Residues 285, Estimated correctness of the model 0.0 % 6 chains (32 residues) have been docked in sequence ------------------------------------------------------ 10354 reflections ( 99.53 % complete ) and 11432 restraints for refining 5106 atoms. 10236 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2163 (Rfree = 0.000) for 5106 atoms. Found 28 (38 requested) and removed 21 (19 requested) atoms. Cycle 42: After refmac, R = 0.2120 (Rfree = 0.000) for 5098 atoms. Found 38 (38 requested) and removed 23 (19 requested) atoms. Cycle 43: After refmac, R = 0.2055 (Rfree = 0.000) for 5094 atoms. Found 28 (38 requested) and removed 20 (19 requested) atoms. Cycle 44: After refmac, R = 0.1937 (Rfree = 0.000) for 5086 atoms. Found 33 (38 requested) and removed 20 (19 requested) atoms. Cycle 45: After refmac, R = 0.1867 (Rfree = 0.000) for 5094 atoms. Found 31 (38 requested) and removed 20 (19 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.25 3.34 Search for helices and strands: 0 residues in 0 chains, 5263 seeds are put forward NCS extension: 17 residues added (3 deleted due to clashes), 5280 seeds are put forward Round 1: 244 peptides, 45 chains. Longest chain 18 peptides. Score 0.334 Round 2: 269 peptides, 45 chains. Longest chain 16 peptides. Score 0.392 Round 3: 283 peptides, 48 chains. Longest chain 13 peptides. Score 0.394 Round 4: 291 peptides, 45 chains. Longest chain 19 peptides. Score 0.440 Round 5: 286 peptides, 47 chains. Longest chain 16 peptides. Score 0.410 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 46, Residues 246, Estimated correctness of the model 0.0 % 5 chains (23 residues) have been docked in sequence Sequence coverage is 9 % Consider running further cycles of model building using 2afb-3_warpNtrace.pdb as input Building loops using Loopy2018 46 chains (246 residues) following loop building 5 chains (23 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 10354 reflections ( 99.53 % complete ) and 11929 restraints for refining 5106 atoms. 10922 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2105 (Rfree = 0.000) for 5106 atoms. Found 0 (38 requested) and removed 19 (19 requested) atoms. Cycle 47: After refmac, R = 0.2128 (Rfree = 0.000) for 5070 atoms. Found 0 (38 requested) and removed 19 (19 requested) atoms. Cycle 48: After refmac, R = 0.1823 (Rfree = 0.000) for 5039 atoms. Found 0 (38 requested) and removed 19 (19 requested) atoms. Cycle 49: After refmac, R = 0.1784 (Rfree = 0.000) for 5016 atoms. Found 0 (37 requested) and removed 18 (18 requested) atoms. TimeTaking 72.77