Sun 23 Dec 22:23:08 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2afb-3.4-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2afb-3.4-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2afb-3.4-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2afb-3.4-parrot-hancs 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/hancs/ArpWArp/wArpResults/WorkingDir/2afb-3.4-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2afb-3.4-parrot-hancs ############### 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 ============================================================ Sun 23 Dec 22:23:18 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/hancs/ArpWArp/wArpResults/WorkingDir/2afb-3.4-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2afb-3.4-parrot-hancs/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-hancs.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-hancs.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 6232 atoms. Observations/parameters ratio is 0.42 ------------------------------------------------------ Starting model: R = 0.3121 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3091 (Rfree = 0.000) for 6232 atoms. Found 47 (47 requested) and removed 49 (23 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.31 3.40 Search for helices and strands: 0 residues in 0 chains, 6343 seeds are put forward NCS extension: 0 residues added, 6343 seeds are put forward Round 1: 245 peptides, 46 chains. Longest chain 11 peptides. Score 0.326 Round 2: 359 peptides, 59 chains. Longest chain 14 peptides. Score 0.454 Round 3: 373 peptides, 53 chains. Longest chain 17 peptides. Score 0.532 Round 4: 429 peptides, 61 chains. Longest chain 22 peptides. Score 0.568 Round 5: 430 peptides, 52 chains. Longest chain 24 peptides. Score 0.634 Taking the results from Round 5 Chains 56, Residues 378, Estimated correctness of the model 39.4 % 6 chains (39 residues) have been docked in sequence ------------------------------------------------------ 10354 reflections ( 99.53 % complete ) and 11076 restraints for refining 5103 atoms. 9519 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2784 (Rfree = 0.000) for 5103 atoms. Found 37 (38 requested) and removed 42 (19 requested) atoms. Cycle 2: After refmac, R = 0.2789 (Rfree = 0.000) for 5007 atoms. Found 28 (38 requested) and removed 38 (19 requested) atoms. Failed to save intermediate PDB Cycle 3: After refmac, R = 0.2498 (Rfree = 0.000) for 4921 atoms. Found 22 (37 requested) and removed 24 (18 requested) atoms. Cycle 4: After refmac, R = 0.2594 (Rfree = 0.000) for 4880 atoms. Found 31 (37 requested) and removed 29 (18 requested) atoms. Cycle 5: After refmac, R = 0.2178 (Rfree = 0.000) for 4849 atoms. Found 16 (36 requested) and removed 21 (18 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.24 3.33 Search for helices and strands: 0 residues in 0 chains, 5032 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 5047 seeds are put forward Round 1: 359 peptides, 55 chains. Longest chain 18 peptides. Score 0.489 Round 2: 395 peptides, 44 chains. Longest chain 31 peptides. Score 0.637 Round 3: 425 peptides, 50 chains. Longest chain 26 peptides. Score 0.640 Round 4: 415 peptides, 39 chains. Longest chain 28 peptides. Score 0.698 Round 5: 403 peptides, 50 chains. Longest chain 20 peptides. Score 0.606 Taking the results from Round 4 Chains 44, Residues 376, Estimated correctness of the model 57.4 % 10 chains (120 residues) have been docked in sequence ------------------------------------------------------ 10354 reflections ( 99.53 % complete ) and 10122 restraints for refining 5105 atoms. 8196 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2604 (Rfree = 0.000) for 5105 atoms. Found 38 (38 requested) and removed 51 (19 requested) atoms. Cycle 7: After refmac, R = 0.2495 (Rfree = 0.000) for 5053 atoms. Found 34 (38 requested) and removed 33 (19 requested) atoms. Cycle 8: After refmac, R = 0.2586 (Rfree = 0.000) for 5035 atoms. Found 38 (38 requested) and removed 32 (19 requested) atoms. Cycle 9: After refmac, R = 0.2391 (Rfree = 0.000) for 5030 atoms. Found 24 (38 requested) and removed 36 (19 requested) atoms. Cycle 10: After refmac, R = 0.2226 (Rfree = 0.000) for 5007 atoms. Found 17 (37 requested) and removed 22 (18 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.26 3.35 Search for helices and strands: 0 residues in 0 chains, 5197 seeds are put forward NCS extension: 29 residues added (1 deleted due to clashes), 5226 seeds are put forward Round 1: 384 peptides, 54 chains. Longest chain 28 peptides. Score 0.544 Round 2: 419 peptides, 57 chains. Longest chain 26 peptides. Score 0.581 Round 3: 422 peptides, 47 chains. Longest chain 26 peptides. Score 0.656 Round 4: 428 peptides, 49 chains. Longest chain 25 peptides. Score 0.651 Round 5: 444 peptides, 48 chains. Longest chain 27 peptides. Score 0.680 Taking the results from Round 5 Chains 52, Residues 396, Estimated correctness of the model 52.6 % 4 chains (74 residues) have been docked in sequence ------------------------------------------------------ 10354 reflections ( 99.53 % complete ) and 10452 restraints for refining 5104 atoms. 8637 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2674 (Rfree = 0.000) for 5104 atoms. Found 25 (38 requested) and removed 38 (19 requested) atoms. Cycle 12: After refmac, R = 0.2657 (Rfree = 0.000) for 5059 atoms. Found 28 (38 requested) and removed 31 (19 requested) atoms. Cycle 13: After refmac, R = 0.2565 (Rfree = 0.000) for 5033 atoms. Found 27 (38 requested) and removed 29 (19 requested) atoms. Cycle 14: After refmac, R = 0.2530 (Rfree = 0.000) for 5020 atoms. Found 28 (37 requested) and removed 33 (18 requested) atoms. Cycle 15: After refmac, R = 0.2370 (Rfree = 0.000) for 5006 atoms. Found 23 (37 requested) and removed 31 (18 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.23 3.32 Search for helices and strands: 0 residues in 0 chains, 5160 seeds are put forward NCS extension: 38 residues added (0 deleted due to clashes), 5198 seeds are put forward Round 1: 382 peptides, 62 chains. Longest chain 18 peptides. Score 0.474 Round 2: 395 peptides, 54 chains. Longest chain 22 peptides. Score 0.563 Round 3: 412 peptides, 57 chains. Longest chain 24 peptides. Score 0.570 Round 4: 415 peptides, 55 chains. Longest chain 24 peptides. Score 0.589 Round 5: 416 peptides, 50 chains. Longest chain 24 peptides. Score 0.627 Taking the results from Round 5 Chains 52, Residues 366, Estimated correctness of the model 37.2 % 3 chains (43 residues) have been docked in sequence ------------------------------------------------------ 10354 reflections ( 99.53 % complete ) and 10974 restraints for refining 5106 atoms. 9386 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2669 (Rfree = 0.000) for 5106 atoms. Found 28 (38 requested) and removed 35 (19 requested) atoms. Cycle 17: After refmac, R = 0.2657 (Rfree = 0.000) for 5067 atoms. Found 32 (38 requested) and removed 29 (19 requested) atoms. Cycle 18: After refmac, R = 0.2407 (Rfree = 0.000) for 5055 atoms. Found 22 (38 requested) and removed 27 (19 requested) atoms. Cycle 19: After refmac, R = 0.2220 (Rfree = 0.000) for 5036 atoms. Found 8 (38 requested) and removed 24 (19 requested) atoms. Cycle 20: After refmac, R = 0.2098 (Rfree = 0.000) for 5014 atoms. Found 4 (37 requested) and removed 21 (18 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.25 3.34 Search for helices and strands: 0 residues in 0 chains, 5173 seeds are put forward NCS extension: 23 residues added (1 deleted due to clashes), 5196 seeds are put forward Round 1: 367 peptides, 60 chains. Longest chain 17 peptides. Score 0.462 Round 2: 395 peptides, 51 chains. Longest chain 19 peptides. Score 0.586 Round 3: 394 peptides, 52 chains. Longest chain 22 peptides. Score 0.577 Round 4: 392 peptides, 52 chains. Longest chain 19 peptides. Score 0.573 Round 5: 391 peptides, 49 chains. Longest chain 22 peptides. Score 0.594 Taking the results from Round 5 Chains 50, Residues 342, Estimated correctness of the model 26.7 % 7 chains (50 residues) have been docked in sequence ------------------------------------------------------ 10354 reflections ( 99.53 % complete ) and 11139 restraints for refining 5106 atoms. 9663 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2465 (Rfree = 0.000) for 5106 atoms. Found 38 (38 requested) and removed 27 (19 requested) atoms. Cycle 22: After refmac, R = 0.2588 (Rfree = 0.000) for 5085 atoms. Found 38 (38 requested) and removed 29 (19 requested) atoms. Cycle 23: After refmac, R = 0.2473 (Rfree = 0.000) for 5070 atoms. Found 38 (38 requested) and removed 26 (19 requested) atoms. Cycle 24: After refmac, R = 0.2115 (Rfree = 0.000) for 5068 atoms. Found 14 (38 requested) and removed 22 (19 requested) atoms. Cycle 25: After refmac, R = 0.2045 (Rfree = 0.000) for 5048 atoms. Found 10 (38 requested) and removed 22 (19 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.27 3.36 Search for helices and strands: 0 residues in 0 chains, 5225 seeds are put forward NCS extension: 19 residues added (1 deleted due to clashes), 5244 seeds are put forward Round 1: 336 peptides, 58 chains. Longest chain 13 peptides. Score 0.416 Round 2: 365 peptides, 53 chains. Longest chain 20 peptides. Score 0.517 Round 3: 385 peptides, 54 chains. Longest chain 26 peptides. Score 0.546 Round 4: 394 peptides, 48 chains. Longest chain 26 peptides. Score 0.606 Round 5: 380 peptides, 50 chains. Longest chain 25 peptides. Score 0.568 Taking the results from Round 4 Chains 51, Residues 346, Estimated correctness of the model 30.6 % 2 chains (36 residues) have been docked in sequence ------------------------------------------------------ 10354 reflections ( 99.53 % complete ) and 11162 restraints for refining 5106 atoms. 9675 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2514 (Rfree = 0.000) for 5106 atoms. Found 36 (38 requested) and removed 34 (19 requested) atoms. Cycle 27: After refmac, R = 0.2375 (Rfree = 0.000) for 5086 atoms. Found 33 (38 requested) and removed 23 (19 requested) atoms. Cycle 28: After refmac, R = 0.2516 (Rfree = 0.000) for 5083 atoms. Found 37 (38 requested) and removed 26 (19 requested) atoms. Cycle 29: After refmac, R = 0.2059 (Rfree = 0.000) for 5077 atoms. Found 14 (38 requested) and removed 22 (19 requested) atoms. Cycle 30: After refmac, R = 0.1971 (Rfree = 0.000) for 5063 atoms. Found 8 (38 requested) and removed 21 (19 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.26 3.35 Search for helices and strands: 0 residues in 0 chains, 5224 seeds are put forward NCS extension: 19 residues added (5 deleted due to clashes), 5243 seeds are put forward Round 1: 337 peptides, 56 chains. Longest chain 15 peptides. Score 0.436 Round 2: 392 peptides, 54 chains. Longest chain 21 peptides. Score 0.558 Round 3: 378 peptides, 53 chains. Longest chain 25 peptides. Score 0.541 Round 4: 381 peptides, 51 chains. Longest chain 23 peptides. Score 0.562 Round 5: 389 peptides, 52 chains. Longest chain 25 peptides. Score 0.568 Taking the results from Round 5 Chains 53, Residues 337, Estimated correctness of the model 17.9 % 4 chains (32 residues) have been docked in sequence ------------------------------------------------------ 10354 reflections ( 99.53 % complete ) and 11383 restraints for refining 5106 atoms. 10001 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2600 (Rfree = 0.000) for 5106 atoms. Found 38 (38 requested) and removed 31 (19 requested) atoms. Cycle 32: After refmac, R = 0.2138 (Rfree = 0.000) for 5087 atoms. Found 15 (38 requested) and removed 26 (19 requested) atoms. Cycle 33: After refmac, R = 0.1990 (Rfree = 0.000) for 5060 atoms. Found 14 (38 requested) and removed 20 (19 requested) atoms. Cycle 34: After refmac, R = 0.2016 (Rfree = 0.000) for 5045 atoms. Found 11 (38 requested) and removed 25 (19 requested) atoms. Cycle 35: After refmac, R = 0.1932 (Rfree = 0.000) for 5026 atoms. Found 14 (37 requested) and removed 18 (18 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.27 3.36 Search for helices and strands: 0 residues in 0 chains, 5170 seeds are put forward NCS extension: 30 residues added (5 deleted due to clashes), 5200 seeds are put forward Round 1: 318 peptides, 58 chains. Longest chain 17 peptides. Score 0.376 Round 2: 356 peptides, 50 chains. Longest chain 22 peptides. Score 0.525 Round 3: 348 peptides, 52 chains. Longest chain 24 peptides. Score 0.493 Round 4: 353 peptides, 51 chains. Longest chain 23 peptides. Score 0.511 Round 5: 369 peptides, 51 chains. Longest chain 24 peptides. Score 0.541 Taking the results from Round 5 Chains 51, Residues 318, Estimated correctness of the model 8.3 % 4 chains (13 residues) have been docked in sequence ------------------------------------------------------ 10354 reflections ( 99.53 % complete ) and 11671 restraints for refining 5106 atoms. 10429 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2468 (Rfree = 0.000) for 5106 atoms. Found 32 (38 requested) and removed 24 (19 requested) atoms. Cycle 37: After refmac, R = 0.2579 (Rfree = 0.000) for 5085 atoms. Found 38 (38 requested) and removed 29 (19 requested) atoms. Cycle 38: After refmac, R = 0.1960 (Rfree = 0.000) for 5074 atoms. Found 16 (38 requested) and removed 21 (19 requested) atoms. Cycle 39: After refmac, R = 0.1898 (Rfree = 0.000) for 5058 atoms. Found 11 (38 requested) and removed 20 (19 requested) atoms. Cycle 40: After refmac, R = 0.1857 (Rfree = 0.000) for 5047 atoms. Found 8 (38 requested) and removed 20 (19 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.27 3.36 Search for helices and strands: 0 residues in 0 chains, 5196 seeds are put forward NCS extension: 22 residues added (1 deleted due to clashes), 5218 seeds are put forward Round 1: 316 peptides, 60 chains. Longest chain 13 peptides. Score 0.353 Round 2: 355 peptides, 56 chains. Longest chain 21 peptides. Score 0.472 Round 3: 359 peptides, 54 chains. Longest chain 22 peptides. Score 0.497 Round 4: 378 peptides, 51 chains. Longest chain 23 peptides. Score 0.557 Round 5: 380 peptides, 55 chains. Longest chain 22 peptides. Score 0.529 Taking the results from Round 4 Chains 52, Residues 327, Estimated correctness of the model 14.0 % 4 chains (31 residues) have been docked in sequence ------------------------------------------------------ 10354 reflections ( 99.53 % complete ) and 11240 restraints for refining 5105 atoms. 9862 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2544 (Rfree = 0.000) for 5105 atoms. Found 38 (38 requested) and removed 31 (19 requested) atoms. Cycle 42: After refmac, R = 0.2235 (Rfree = 0.000) for 5102 atoms. Found 36 (38 requested) and removed 29 (19 requested) atoms. Cycle 43: After refmac, R = 0.2186 (Rfree = 0.000) for 5096 atoms. Found 38 (38 requested) and removed 24 (19 requested) atoms. Cycle 44: After refmac, R = 0.1798 (Rfree = 0.000) for 5103 atoms. Found 4 (38 requested) and removed 21 (19 requested) atoms. Cycle 45: After refmac, R = 0.1738 (Rfree = 0.000) for 5082 atoms. Found 9 (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, 5244 seeds are put forward NCS extension: 21 residues added (0 deleted due to clashes), 5265 seeds are put forward Round 1: 310 peptides, 56 chains. Longest chain 18 peptides. Score 0.378 Round 2: 343 peptides, 56 chains. Longest chain 25 peptides. Score 0.448 Round 3: 335 peptides, 55 chains. Longest chain 20 peptides. Score 0.441 Round 4: 342 peptides, 54 chains. Longest chain 26 peptides. Score 0.464 Round 5: 336 peptides, 52 chains. Longest chain 25 peptides. Score 0.469 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 52, Residues 284, Estimated correctness of the model 0.0 % 6 chains (39 residues) have been docked in sequence Sequence coverage is 13 % Consider running further cycles of model building using 2afb-3_warpNtrace.pdb as input Building loops using Loopy2018 Built loop between residues 296 A and 309 A 50 chains (294 residues) following loop building 5 chains (51 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 10354 reflections ( 99.53 % complete ) and 11325 restraints for refining 5106 atoms. 10043 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2332 (Rfree = 0.000) for 5106 atoms. Found 0 (38 requested) and removed 19 (19 requested) atoms. Cycle 47: After refmac, R = 0.2018 (Rfree = 0.000) for 5072 atoms. Found 0 (38 requested) and removed 19 (19 requested) atoms. Cycle 48: After refmac, R = 0.1895 (Rfree = 0.000) for 5044 atoms. Found 0 (38 requested) and removed 19 (19 requested) atoms. Cycle 49: After refmac, R = 0.1854 (Rfree = 0.000) for 5024 atoms. TimeTaking 82.45