null Sun 23 Dec 22:22:59 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 2a9v-2.2-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2a9v-2.2-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2a9v-2.2-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2a9v-2.2-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/2a9v-2.2-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2a9v-2.2-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 22:23:07 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/2a9v-2.2-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2a9v-2.2-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 661 and 0 Target number of residues in the AU: 661 Target solvent content: 0.5129 Checking the provided sequence file Detected sequence length: 212 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 848 Adjusted target solvent content: 0.38 Input MTZ file: 2a9v-2.2-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: 18 Cell parameters: 275.612 39.042 68.255 90.000 90.000 90.000 Input sequence file: 2a9v-2.2-parrot-hancs.fasta_lf Building free atoms model in initial map for 6784 target number of atoms Had to go as low as 0.50 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 1 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: 137.806 2.200 Wilson plot Bfac: 26.11 33709 reflections ( 87.11 % complete ) and 0 restraints for refining 7557 atoms. Observations/parameters ratio is 1.12 ------------------------------------------------------ Starting model: R = 0.3823 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3262 (Rfree = 0.000) for 7557 atoms. Found 113 (197 requested) and removed 149 (98 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.30 2.71 NCS extension: 0 residues added, 7521 seeds are put forward Round 1: 283 peptides, 63 chains. Longest chain 8 peptides. Score 0.245 Round 2: 318 peptides, 62 chains. Longest chain 11 peptides. Score 0.338 Round 3: 318 peptides, 57 chains. Longest chain 12 peptides. Score 0.386 Round 4: 315 peptides, 54 chains. Longest chain 15 peptides. Score 0.407 Round 5: 330 peptides, 50 chains. Longest chain 19 peptides. Score 0.475 Taking the results from Round 5 Chains 50, Residues 280, Estimated correctness of the model 70.4 % 3 chains (12 residues) have been docked in sequence ------------------------------------------------------ 33709 reflections ( 87.11 % complete ) and 14605 restraints for refining 6477 atoms. 13516 conditional restraints added. Observations/parameters ratio is 1.30 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3366 (Rfree = 0.000) for 6477 atoms. Found 110 (169 requested) and removed 93 (84 requested) atoms. Cycle 2: After refmac, R = 0.3129 (Rfree = 0.000) for 6490 atoms. Found 92 (169 requested) and removed 89 (84 requested) atoms. Cycle 3: After refmac, R = 0.3026 (Rfree = 0.000) for 6480 atoms. Found 74 (169 requested) and removed 84 (84 requested) atoms. Cycle 4: After refmac, R = 0.2928 (Rfree = 0.000) for 6461 atoms. Found 57 (168 requested) and removed 84 (84 requested) atoms. Cycle 5: After refmac, R = 0.2856 (Rfree = 0.000) for 6426 atoms. Found 64 (167 requested) and removed 83 (83 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.18 2.57 NCS extension: 0 residues added, 6446 seeds are put forward Round 1: 310 peptides, 56 chains. Longest chain 14 peptides. Score 0.377 Round 2: 307 peptides, 51 chains. Longest chain 13 peptides. Score 0.418 Round 3: 330 peptides, 46 chains. Longest chain 18 peptides. Score 0.509 Round 4: 324 peptides, 48 chains. Longest chain 18 peptides. Score 0.480 Round 5: 314 peptides, 47 chains. Longest chain 18 peptides. Score 0.469 Taking the results from Round 3 Chains 47, Residues 284, Estimated correctness of the model 73.9 % 4 chains (26 residues) have been docked in sequence ------------------------------------------------------ 33709 reflections ( 87.11 % complete ) and 14145 restraints for refining 6454 atoms. 12978 conditional restraints added. Observations/parameters ratio is 1.31 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3030 (Rfree = 0.000) for 6454 atoms. Found 105 (168 requested) and removed 89 (84 requested) atoms. Cycle 7: After refmac, R = 0.2844 (Rfree = 0.000) for 6462 atoms. Found 80 (168 requested) and removed 84 (84 requested) atoms. Cycle 8: After refmac, R = 0.2731 (Rfree = 0.000) for 6453 atoms. Found 75 (168 requested) and removed 67 (84 requested) atoms. Cycle 9: After refmac, R = 0.2655 (Rfree = 0.000) for 6457 atoms. Found 55 (168 requested) and removed 57 (84 requested) atoms. Cycle 10: After refmac, R = 0.2587 (Rfree = 0.000) for 6448 atoms. Found 71 (168 requested) and removed 46 (84 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.15 2.53 NCS extension: 4 residues added (0 deleted due to clashes), 6494 seeds are put forward Round 1: 295 peptides, 52 chains. Longest chain 15 peptides. Score 0.382 Round 2: 304 peptides, 47 chains. Longest chain 13 peptides. Score 0.448 Round 3: 310 peptides, 45 chains. Longest chain 20 peptides. Score 0.479 Round 4: 317 peptides, 48 chains. Longest chain 15 peptides. Score 0.466 Round 5: 329 peptides, 52 chains. Longest chain 19 peptides. Score 0.455 Taking the results from Round 3 Chains 46, Residues 265, Estimated correctness of the model 70.9 % 4 chains (34 residues) have been docked in sequence ------------------------------------------------------ 33709 reflections ( 87.11 % complete ) and 14079 restraints for refining 6477 atoms. 12959 conditional restraints added. Observations/parameters ratio is 1.30 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2748 (Rfree = 0.000) for 6477 atoms. Found 112 (169 requested) and removed 90 (84 requested) atoms. Cycle 12: After refmac, R = 0.2574 (Rfree = 0.000) for 6497 atoms. Found 76 (169 requested) and removed 73 (84 requested) atoms. Cycle 13: After refmac, R = 0.2500 (Rfree = 0.000) for 6496 atoms. Found 85 (169 requested) and removed 57 (84 requested) atoms. Cycle 14: After refmac, R = 0.2441 (Rfree = 0.000) for 6522 atoms. Found 71 (170 requested) and removed 42 (85 requested) atoms. Cycle 15: After refmac, R = 0.2397 (Rfree = 0.000) for 6549 atoms. Found 75 (171 requested) and removed 26 (85 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.13 2.51 NCS extension: 5 residues added (1 deleted due to clashes), 6618 seeds are put forward Round 1: 321 peptides, 59 chains. Longest chain 14 peptides. Score 0.373 Round 2: 331 peptides, 48 chains. Longest chain 21 peptides. Score 0.494 Round 3: 330 peptides, 51 chains. Longest chain 16 peptides. Score 0.466 Round 4: 325 peptides, 48 chains. Longest chain 17 peptides. Score 0.482 Round 5: 325 peptides, 52 chains. Longest chain 15 peptides. Score 0.447 Taking the results from Round 2 Chains 48, Residues 283, Estimated correctness of the model 72.4 % 3 chains (13 residues) have been docked in sequence ------------------------------------------------------ 33709 reflections ( 87.11 % complete ) and 13778 restraints for refining 6476 atoms. 12666 conditional restraints added. Observations/parameters ratio is 1.30 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2593 (Rfree = 0.000) for 6476 atoms. Found 136 (169 requested) and removed 84 (84 requested) atoms. Cycle 17: After refmac, R = 0.2465 (Rfree = 0.000) for 6525 atoms. Found 94 (170 requested) and removed 43 (85 requested) atoms. Cycle 18: After refmac, R = 0.2384 (Rfree = 0.000) for 6574 atoms. Found 86 (171 requested) and removed 52 (85 requested) atoms. Cycle 19: After refmac, R = 0.2338 (Rfree = 0.000) for 6606 atoms. Found 87 (172 requested) and removed 48 (86 requested) atoms. Cycle 20: After refmac, R = 0.2290 (Rfree = 0.000) for 6641 atoms. Found 89 (173 requested) and removed 32 (86 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.14 2.52 NCS extension: 10 residues added (0 deleted due to clashes), 6730 seeds are put forward Round 1: 291 peptides, 54 chains. Longest chain 10 peptides. Score 0.354 Round 2: 301 peptides, 48 chains. Longest chain 24 peptides. Score 0.433 Round 3: 310 peptides, 50 chains. Longest chain 15 peptides. Score 0.433 Round 4: 311 peptides, 47 chains. Longest chain 15 peptides. Score 0.463 Round 5: 304 peptides, 45 chains. Longest chain 24 peptides. Score 0.467 Taking the results from Round 5 Chains 47, Residues 259, Estimated correctness of the model 69.6 % 3 chains (24 residues) have been docked in sequence ------------------------------------------------------ 33709 reflections ( 87.11 % complete ) and 13434 restraints for refining 6477 atoms. 12390 conditional restraints added. Observations/parameters ratio is 1.30 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2568 (Rfree = 0.000) for 6477 atoms. Found 165 (169 requested) and removed 90 (84 requested) atoms. Cycle 22: After refmac, R = 0.2392 (Rfree = 0.000) for 6550 atoms. Found 111 (171 requested) and removed 36 (85 requested) atoms. Cycle 23: After refmac, R = 0.2316 (Rfree = 0.000) for 6625 atoms. Found 105 (172 requested) and removed 39 (86 requested) atoms. Cycle 24: After refmac, R = 0.2273 (Rfree = 0.000) for 6689 atoms. Found 89 (174 requested) and removed 58 (87 requested) atoms. Cycle 25: After refmac, R = 0.2251 (Rfree = 0.000) for 6720 atoms. Found 78 (175 requested) and removed 66 (87 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.15 2.53 NCS extension: 0 residues added, 6762 seeds are put forward Round 1: 274 peptides, 46 chains. Longest chain 23 peptides. Score 0.393 Round 2: 298 peptides, 45 chains. Longest chain 18 peptides. Score 0.454 Round 3: 291 peptides, 43 chains. Longest chain 22 peptides. Score 0.458 Round 4: 292 peptides, 43 chains. Longest chain 13 peptides. Score 0.460 Round 5: 297 peptides, 46 chains. Longest chain 19 peptides. Score 0.443 Taking the results from Round 4 Chains 44, Residues 249, Estimated correctness of the model 68.9 % 1 chains (11 residues) have been docked in sequence ------------------------------------------------------ 33709 reflections ( 87.11 % complete ) and 13413 restraints for refining 6477 atoms. 12435 conditional restraints added. Observations/parameters ratio is 1.30 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2475 (Rfree = 0.000) for 6477 atoms. Found 169 (169 requested) and removed 64 (84 requested) atoms. Cycle 27: After refmac, R = 0.2355 (Rfree = 0.000) for 6582 atoms. Found 142 (171 requested) and removed 52 (85 requested) atoms. Cycle 28: After refmac, R = 0.2267 (Rfree = 0.000) for 6670 atoms. Found 100 (174 requested) and removed 49 (87 requested) atoms. Cycle 29: After refmac, R = 0.2198 (Rfree = 0.000) for 6721 atoms. Found 93 (175 requested) and removed 55 (87 requested) atoms. Cycle 30: After refmac, R = 0.2167 (Rfree = 0.000) for 6758 atoms. Found 91 (176 requested) and removed 67 (88 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.14 2.52 NCS extension: 0 residues added, 6799 seeds are put forward Round 1: 264 peptides, 47 chains. Longest chain 15 peptides. Score 0.361 Round 2: 276 peptides, 43 chains. Longest chain 14 peptides. Score 0.426 Round 3: 296 peptides, 43 chains. Longest chain 19 peptides. Score 0.468 Round 4: 290 peptides, 43 chains. Longest chain 17 peptides. Score 0.456 Round 5: 283 peptides, 44 chains. Longest chain 19 peptides. Score 0.432 Taking the results from Round 3 Chains 43, Residues 253, Estimated correctness of the model 69.7 % 3 chains (13 residues) have been docked in sequence ------------------------------------------------------ 33709 reflections ( 87.11 % complete ) and 13152 restraints for refining 6477 atoms. 12140 conditional restraints added. Observations/parameters ratio is 1.30 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2416 (Rfree = 0.000) for 6477 atoms. Found 169 (169 requested) and removed 55 (84 requested) atoms. Cycle 32: After refmac, R = 0.2310 (Rfree = 0.000) for 6591 atoms. Found 142 (172 requested) and removed 31 (86 requested) atoms. Cycle 33: After refmac, R = 0.2212 (Rfree = 0.000) for 6701 atoms. Found 96 (174 requested) and removed 55 (87 requested) atoms. Cycle 34: After refmac, R = 0.2176 (Rfree = 0.000) for 6741 atoms. Found 108 (176 requested) and removed 69 (88 requested) atoms. Cycle 35: After refmac, R = 0.2149 (Rfree = 0.000) for 6779 atoms. Found 110 (176 requested) and removed 81 (88 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.12 2.50 NCS extension: 0 residues added, 6827 seeds are put forward Round 1: 261 peptides, 47 chains. Longest chain 14 peptides. Score 0.354 Round 2: 281 peptides, 41 chains. Longest chain 22 peptides. Score 0.456 Round 3: 281 peptides, 43 chains. Longest chain 17 peptides. Score 0.437 Round 4: 278 peptides, 42 chains. Longest chain 16 peptides. Score 0.440 Round 5: 269 peptides, 42 chains. Longest chain 18 peptides. Score 0.421 Taking the results from Round 2 Chains 41, Residues 240, Estimated correctness of the model 68.5 % 3 chains (13 residues) have been docked in sequence ------------------------------------------------------ 33709 reflections ( 87.11 % complete ) and 13250 restraints for refining 6477 atoms. 12311 conditional restraints added. Observations/parameters ratio is 1.30 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2333 (Rfree = 0.000) for 6477 atoms. Found 169 (169 requested) and removed 54 (84 requested) atoms. Cycle 37: After refmac, R = 0.2250 (Rfree = 0.000) for 6591 atoms. Found 170 (172 requested) and removed 39 (86 requested) atoms. Cycle 38: After refmac, R = 0.2184 (Rfree = 0.000) for 6720 atoms. Found 113 (175 requested) and removed 67 (87 requested) atoms. Cycle 39: After refmac, R = 0.2161 (Rfree = 0.000) for 6764 atoms. Found 124 (176 requested) and removed 69 (88 requested) atoms. Cycle 40: After refmac, R = 0.2111 (Rfree = 0.000) for 6818 atoms. Found 125 (177 requested) and removed 90 (88 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.14 2.52 NCS extension: 0 residues added, 6871 seeds are put forward Round 1: 247 peptides, 44 chains. Longest chain 18 peptides. Score 0.351 Round 2: 263 peptides, 42 chains. Longest chain 22 peptides. Score 0.408 Round 3: 266 peptides, 37 chains. Longest chain 22 peptides. Score 0.462 Round 4: 256 peptides, 39 chains. Longest chain 12 peptides. Score 0.422 Round 5: 264 peptides, 37 chains. Longest chain 22 peptides. Score 0.458 Taking the results from Round 3 Chains 37, Residues 229, Estimated correctness of the model 69.1 % 4 chains (25 residues) have been docked in sequence ------------------------------------------------------ 33709 reflections ( 87.11 % complete ) and 13060 restraints for refining 6477 atoms. 12110 conditional restraints added. Observations/parameters ratio is 1.30 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2368 (Rfree = 0.000) for 6477 atoms. Found 169 (169 requested) and removed 69 (84 requested) atoms. Cycle 42: After refmac, R = 0.2256 (Rfree = 0.000) for 6577 atoms. Found 171 (171 requested) and removed 34 (85 requested) atoms. Cycle 43: After refmac, R = 0.2156 (Rfree = 0.000) for 6714 atoms. Found 110 (175 requested) and removed 63 (87 requested) atoms. Cycle 44: After refmac, R = 0.2125 (Rfree = 0.000) for 6760 atoms. Found 126 (176 requested) and removed 72 (88 requested) atoms. Cycle 45: After refmac, R = 0.2093 (Rfree = 0.000) for 6813 atoms. Found 125 (177 requested) and removed 91 (88 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.14 2.52 NCS extension: 8 residues added (0 deleted due to clashes), 6870 seeds are put forward Round 1: 254 peptides, 47 chains. Longest chain 13 peptides. Score 0.337 Round 2: 261 peptides, 43 chains. Longest chain 13 peptides. Score 0.393 Round 3: 255 peptides, 43 chains. Longest chain 17 peptides. Score 0.380 Round 4: 253 peptides, 42 chains. Longest chain 14 peptides. Score 0.385 Round 5: 265 peptides, 43 chains. Longest chain 13 peptides. Score 0.402 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 43, Residues 222, Estimated correctness of the model 62.5 % 3 chains (19 residues) have been docked in sequence Sequence coverage is 8 % Consider running further cycles of model building using 2a9v-2_warpNtrace.pdb as input Building loops using Loopy2018 43 chains (222 residues) following loop building 3 chains (19 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 33709 reflections ( 87.11 % complete ) and 12946 restraints for refining 6477 atoms. 12040 conditional restraints added. Observations/parameters ratio is 1.30 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2334 (Rfree = 0.000) for 6477 atoms. Found 0 (169 requested) and removed 16 (84 requested) atoms. Cycle 47: After refmac, R = 0.2237 (Rfree = 0.000) for 6459 atoms. Found 0 (168 requested) and removed 7 (84 requested) atoms. Cycle 48: After refmac, R = 0.2190 (Rfree = 0.000) for 6451 atoms. Found 0 (168 requested) and removed 4 (84 requested) atoms. Cycle 49: After refmac, R = 0.2162 (Rfree = 0.000) for 6447 atoms. Found 0 (168 requested) and removed 4 (84 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 23:44:15 GMT 2018 Job finished. TimeTaking 81.28 Used memory is bytes: 2863728