Mon 24 Dec 07:55:09 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 2iiu-3.2-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2iiu-3.2-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2iiu-3.2-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2iiu-3.2-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/2iiu-3.2-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2iiu-3.2-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 07:55:13 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/2iiu-3.2-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2iiu-3.2-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 543 and 0 Target number of residues in the AU: 543 Target solvent content: 0.6149 Checking the provided sequence file Detected sequence length: 227 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 3 Adjusted target number of residues: 681 Adjusted target solvent content: 0.52 Input MTZ file: 2iiu-3.2-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: 99.900 99.900 397.311 90.000 90.000 120.000 Input sequence file: 2iiu-3.2-parrot-noncs.fasta_lf Building free atoms model in initial map for 5448 target number of atoms Had to go as low as 0.75 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: 132.437 3.200 Wilson plot Bfac: 58.76 12997 reflections ( 99.27 % complete ) and 0 restraints for refining 6043 atoms. Observations/parameters ratio is 0.54 ------------------------------------------------------ Starting model: R = 0.3405 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2996 (Rfree = 0.000) for 6043 atoms. Found 54 (54 requested) and removed 79 (27 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.06 2.98 Search for helices and strands: 0 residues in 0 chains, 6191 seeds are put forward NCS extension: 0 residues added, 6191 seeds are put forward Round 1: 247 peptides, 52 chains. Longest chain 10 peptides. Score 0.266 Round 2: 304 peptides, 55 chains. Longest chain 19 peptides. Score 0.368 Round 3: 324 peptides, 56 chains. Longest chain 16 peptides. Score 0.401 Round 4: 332 peptides, 60 chains. Longest chain 13 peptides. Score 0.382 Round 5: 313 peptides, 52 chains. Longest chain 18 peptides. Score 0.414 Taking the results from Round 5 Chains 54, Residues 261, Estimated correctness of the model 0.0 % 2 chains (22 residues) have been docked in sequence ------------------------------------------------------ 12997 reflections ( 99.27 % complete ) and 11071 restraints for refining 4974 atoms. 9993 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2609 (Rfree = 0.000) for 4974 atoms. Found 44 (44 requested) and removed 34 (22 requested) atoms. Failed to save intermediate PDB Cycle 2: After refmac, R = 0.2421 (Rfree = 0.000) for 4915 atoms. Found 32 (44 requested) and removed 31 (22 requested) atoms. Cycle 3: After refmac, R = 0.2259 (Rfree = 0.000) for 4888 atoms. Found 21 (44 requested) and removed 26 (22 requested) atoms. Cycle 4: After refmac, R = 0.2175 (Rfree = 0.000) for 4866 atoms. Found 13 (43 requested) and removed 28 (21 requested) atoms. Cycle 5: After refmac, R = 0.2064 (Rfree = 0.000) for 4843 atoms. Found 12 (43 requested) and removed 23 (21 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.05 2.97 Search for helices and strands: 0 residues in 0 chains, 5056 seeds are put forward NCS extension: 6 residues added (0 deleted due to clashes), 5062 seeds are put forward Round 1: 347 peptides, 61 chains. Longest chain 15 peptides. Score 0.404 Round 2: 370 peptides, 59 chains. Longest chain 19 peptides. Score 0.467 Round 3: 364 peptides, 52 chains. Longest chain 24 peptides. Score 0.514 Round 4: 368 peptides, 56 chains. Longest chain 22 peptides. Score 0.488 Round 5: 369 peptides, 52 chains. Longest chain 28 peptides. Score 0.523 Taking the results from Round 5 Chains 52, Residues 317, Estimated correctness of the model 18.7 % 2 chains (33 residues) have been docked in sequence ------------------------------------------------------ 12997 reflections ( 99.27 % complete ) and 10841 restraints for refining 4973 atoms. 9500 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2495 (Rfree = 0.000) for 4973 atoms. Found 44 (44 requested) and removed 35 (22 requested) atoms. Cycle 7: After refmac, R = 0.2274 (Rfree = 0.000) for 4957 atoms. Found 22 (44 requested) and removed 27 (22 requested) atoms. Cycle 8: After refmac, R = 0.2179 (Rfree = 0.000) for 4944 atoms. Found 17 (44 requested) and removed 23 (22 requested) atoms. Cycle 9: After refmac, R = 0.2105 (Rfree = 0.000) for 4930 atoms. Found 19 (44 requested) and removed 24 (22 requested) atoms. Cycle 10: After refmac, R = 0.2048 (Rfree = 0.000) for 4919 atoms. Found 4 (44 requested) and removed 22 (22 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.08 3.00 Search for helices and strands: 0 residues in 0 chains, 5103 seeds are put forward NCS extension: 12 residues added (6 deleted due to clashes), 5115 seeds are put forward Round 1: 339 peptides, 60 chains. Longest chain 16 peptides. Score 0.397 Round 2: 374 peptides, 57 chains. Longest chain 19 peptides. Score 0.491 Round 3: 385 peptides, 58 chains. Longest chain 21 peptides. Score 0.504 Round 4: 388 peptides, 56 chains. Longest chain 23 peptides. Score 0.525 Round 5: 382 peptides, 58 chains. Longest chain 18 peptides. Score 0.498 Taking the results from Round 4 Chains 56, Residues 332, Estimated correctness of the model 19.3 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ 12997 reflections ( 99.27 % complete ) and 10898 restraints for refining 4973 atoms. 9592 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2366 (Rfree = 0.000) for 4973 atoms. Found 37 (44 requested) and removed 28 (22 requested) atoms. Cycle 12: After refmac, R = 0.2127 (Rfree = 0.000) for 4961 atoms. Found 16 (44 requested) and removed 28 (22 requested) atoms. Cycle 13: After refmac, R = 0.2074 (Rfree = 0.000) for 4943 atoms. Found 7 (44 requested) and removed 22 (22 requested) atoms. Cycle 14: After refmac, R = 0.2058 (Rfree = 0.000) for 4922 atoms. Found 7 (44 requested) and removed 22 (22 requested) atoms. Cycle 15: After refmac, R = 0.2072 (Rfree = 0.000) for 4905 atoms. Found 4 (44 requested) and removed 22 (22 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.09 3.01 Search for helices and strands: 0 residues in 0 chains, 5136 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 5150 seeds are put forward Round 1: 333 peptides, 63 chains. Longest chain 14 peptides. Score 0.357 Round 2: 361 peptides, 60 chains. Longest chain 14 peptides. Score 0.441 Round 3: 389 peptides, 61 chains. Longest chain 14 peptides. Score 0.487 Round 4: 369 peptides, 58 chains. Longest chain 22 peptides. Score 0.474 Round 5: 370 peptides, 56 chains. Longest chain 20 peptides. Score 0.492 Taking the results from Round 5 Chains 56, Residues 314, Estimated correctness of the model 8.7 % 2 chains (15 residues) have been docked in sequence ------------------------------------------------------ 12997 reflections ( 99.27 % complete ) and 10964 restraints for refining 4974 atoms. 9717 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2359 (Rfree = 0.000) for 4974 atoms. Found 34 (44 requested) and removed 25 (22 requested) atoms. Cycle 17: After refmac, R = 0.2180 (Rfree = 0.000) for 4966 atoms. Found 12 (44 requested) and removed 24 (22 requested) atoms. Cycle 18: After refmac, R = 0.2144 (Rfree = 0.000) for 4943 atoms. Found 10 (44 requested) and removed 22 (22 requested) atoms. Cycle 19: After refmac, R = 0.2141 (Rfree = 0.000) for 4926 atoms. Found 8 (44 requested) and removed 23 (22 requested) atoms. Cycle 20: After refmac, R = 0.2075 (Rfree = 0.000) for 4905 atoms. Found 10 (44 requested) and removed 23 (22 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.09 3.01 Search for helices and strands: 0 residues in 0 chains, 5112 seeds are put forward NCS extension: 16 residues added (2 deleted due to clashes), 5128 seeds are put forward Round 1: 299 peptides, 59 chains. Longest chain 14 peptides. Score 0.319 Round 2: 358 peptides, 62 chains. Longest chain 13 peptides. Score 0.418 Round 3: 359 peptides, 55 chains. Longest chain 22 peptides. Score 0.480 Round 4: 356 peptides, 54 chains. Longest chain 14 peptides. Score 0.482 Round 5: 373 peptides, 57 chains. Longest chain 14 peptides. Score 0.490 Taking the results from Round 5 Chains 57, Residues 316, Estimated correctness of the model 8.1 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 12997 reflections ( 99.27 % complete ) and 11111 restraints for refining 4973 atoms. 9904 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2343 (Rfree = 0.000) for 4973 atoms. Found 34 (44 requested) and removed 27 (22 requested) atoms. Cycle 22: After refmac, R = 0.2191 (Rfree = 0.000) for 4970 atoms. Found 17 (44 requested) and removed 24 (22 requested) atoms. Cycle 23: After refmac, R = 0.2125 (Rfree = 0.000) for 4954 atoms. Found 21 (44 requested) and removed 22 (22 requested) atoms. Cycle 24: After refmac, R = 0.2057 (Rfree = 0.000) for 4947 atoms. Found 8 (44 requested) and removed 24 (22 requested) atoms. Cycle 25: After refmac, R = 0.2049 (Rfree = 0.000) for 4924 atoms. Found 10 (44 requested) and removed 23 (22 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.05 2.97 Search for helices and strands: 0 residues in 0 chains, 5112 seeds are put forward NCS extension: 11 residues added (6 deleted due to clashes), 5123 seeds are put forward Round 1: 339 peptides, 62 chains. Longest chain 14 peptides. Score 0.379 Round 2: 362 peptides, 55 chains. Longest chain 18 peptides. Score 0.485 Round 3: 354 peptides, 52 chains. Longest chain 22 peptides. Score 0.495 Round 4: 346 peptides, 53 chains. Longest chain 19 peptides. Score 0.472 Round 5: 353 peptides, 55 chains. Longest chain 14 peptides. Score 0.468 Taking the results from Round 3 Chains 52, Residues 302, Estimated correctness of the model 9.7 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 12997 reflections ( 99.27 % complete ) and 11147 restraints for refining 4974 atoms. 9991 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2248 (Rfree = 0.000) for 4974 atoms. Found 38 (44 requested) and removed 24 (22 requested) atoms. Cycle 27: After refmac, R = 0.2120 (Rfree = 0.000) for 4975 atoms. Found 12 (44 requested) and removed 25 (22 requested) atoms. Cycle 28: After refmac, R = 0.2098 (Rfree = 0.000) for 4957 atoms. Found 18 (44 requested) and removed 25 (22 requested) atoms. Cycle 29: After refmac, R = 0.2068 (Rfree = 0.000) for 4945 atoms. Found 16 (44 requested) and removed 23 (22 requested) atoms. Cycle 30: After refmac, R = 0.2035 (Rfree = 0.000) for 4935 atoms. Found 11 (44 requested) and removed 23 (22 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.06 2.98 Search for helices and strands: 0 residues in 0 chains, 5149 seeds are put forward NCS extension: 12 residues added (2 deleted due to clashes), 5161 seeds are put forward Round 1: 298 peptides, 55 chains. Longest chain 15 peptides. Score 0.354 Round 2: 331 peptides, 57 chains. Longest chain 12 peptides. Score 0.407 Round 3: 352 peptides, 60 chains. Longest chain 16 peptides. Score 0.423 Round 4: 347 peptides, 53 chains. Longest chain 18 peptides. Score 0.474 Round 5: 339 peptides, 54 chains. Longest chain 19 peptides. Score 0.449 Taking the results from Round 4 Chains 53, Residues 294, Estimated correctness of the model 2.7 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 12997 reflections ( 99.27 % complete ) and 11172 restraints for refining 4974 atoms. 10049 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2216 (Rfree = 0.000) for 4974 atoms. Found 39 (44 requested) and removed 25 (22 requested) atoms. Cycle 32: After refmac, R = 0.2073 (Rfree = 0.000) for 4976 atoms. Found 14 (44 requested) and removed 23 (22 requested) atoms. Cycle 33: After refmac, R = 0.2025 (Rfree = 0.000) for 4959 atoms. Found 15 (44 requested) and removed 22 (22 requested) atoms. Cycle 34: After refmac, R = 0.2188 (Rfree = 0.000) for 4943 atoms. Found 27 (44 requested) and removed 22 (22 requested) atoms. Cycle 35: After refmac, R = 0.1932 (Rfree = 0.000) for 4939 atoms. Found 8 (44 requested) and removed 22 (22 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.06 2.98 Search for helices and strands: 0 residues in 0 chains, 5091 seeds are put forward NCS extension: 23 residues added (3 deleted due to clashes), 5114 seeds are put forward Round 1: 312 peptides, 62 chains. Longest chain 12 peptides. Score 0.320 Round 2: 344 peptides, 57 chains. Longest chain 14 peptides. Score 0.433 Round 3: 350 peptides, 56 chains. Longest chain 14 peptides. Score 0.454 Round 4: 358 peptides, 56 chains. Longest chain 17 peptides. Score 0.469 Round 5: 342 peptides, 54 chains. Longest chain 13 peptides. Score 0.455 Taking the results from Round 4 Chains 59, Residues 302, Estimated correctness of the model 1.0 % 2 chains (25 residues) have been docked in sequence ------------------------------------------------------ 12997 reflections ( 99.27 % complete ) and 10842 restraints for refining 4973 atoms. 9587 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2216 (Rfree = 0.000) for 4973 atoms. Found 41 (44 requested) and removed 25 (22 requested) atoms. Cycle 37: After refmac, R = 0.2053 (Rfree = 0.000) for 4978 atoms. Found 15 (44 requested) and removed 25 (22 requested) atoms. Cycle 38: After refmac, R = 0.2242 (Rfree = 0.000) for 4958 atoms. Found 34 (44 requested) and removed 27 (22 requested) atoms. Cycle 39: After refmac, R = 0.2039 (Rfree = 0.000) for 4951 atoms. Found 29 (44 requested) and removed 24 (22 requested) atoms. Cycle 40: After refmac, R = 0.1871 (Rfree = 0.000) for 4950 atoms. Found 13 (44 requested) and removed 25 (22 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.03 2.95 Search for helices and strands: 0 residues in 0 chains, 5139 seeds are put forward NCS extension: 22 residues added (2 deleted due to clashes), 5161 seeds are put forward Round 1: 280 peptides, 55 chains. Longest chain 9 peptides. Score 0.314 Round 2: 320 peptides, 56 chains. Longest chain 12 peptides. Score 0.393 Round 3: 337 peptides, 57 chains. Longest chain 13 peptides. Score 0.419 Round 4: 328 peptides, 51 chains. Longest chain 15 peptides. Score 0.454 Round 5: 336 peptides, 54 chains. Longest chain 15 peptides. Score 0.443 Taking the results from Round 4 Chains 51, Residues 277, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 12997 reflections ( 99.27 % complete ) and 11086 restraints for refining 4974 atoms. 10008 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2109 (Rfree = 0.000) for 4974 atoms. Found 43 (44 requested) and removed 24 (22 requested) atoms. Cycle 42: After refmac, R = 0.2282 (Rfree = 0.000) for 4978 atoms. Found 37 (44 requested) and removed 25 (22 requested) atoms. Cycle 43: After refmac, R = 0.1863 (Rfree = 0.000) for 4980 atoms. Found 20 (44 requested) and removed 26 (22 requested) atoms. Cycle 44: After refmac, R = 0.1819 (Rfree = 0.000) for 4968 atoms. Found 17 (44 requested) and removed 24 (22 requested) atoms. Cycle 45: After refmac, R = 0.1902 (Rfree = 0.000) for 4955 atoms. Found 19 (44 requested) and removed 25 (22 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.05 2.97 Search for helices and strands: 0 residues in 0 chains, 5141 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 5156 seeds are put forward Round 1: 261 peptides, 52 chains. Longest chain 9 peptides. Score 0.299 Round 2: 312 peptides, 54 chains. Longest chain 16 peptides. Score 0.394 Round 3: 305 peptides, 53 chains. Longest chain 12 peptides. Score 0.388 Round 4: 311 peptides, 48 chains. Longest chain 18 peptides. Score 0.446 Round 5: 314 peptides, 50 chains. Longest chain 17 peptides. Score 0.434 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 49, Residues 263, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence Sequence coverage is 3 % Consider running further cycles of model building using 2iiu-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 12997 reflections ( 99.27 % complete ) and 11085 restraints for refining 4974 atoms. 10053 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2037 (Rfree = 0.000) for 4974 atoms. Found 0 (44 requested) and removed 21 (22 requested) atoms. Cycle 47: After refmac, R = 0.1986 (Rfree = 0.000) for 4949 atoms. Found 0 (44 requested) and removed 11 (22 requested) atoms. Cycle 48: After refmac, R = 0.2007 (Rfree = 0.000) for 4933 atoms. Found 0 (44 requested) and removed 18 (22 requested) atoms. Cycle 49: After refmac, R = 0.1964 (Rfree = 0.000) for 4912 atoms. Found 0 (44 requested) and removed 15 (22 requested) atoms. Writing output files ... Failed to save intermediate PDB TimeTaking 61.38