Sun 23 Dec 22:22:43 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 2h1q-4.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2h1q-4.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2h1q-4.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2h1q-4.0-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/2h1q-4.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2h1q-4.0-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 22:22:53 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/2h1q-4.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2h1q-4.0-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 372 and 0 Target number of residues in the AU: 372 Target solvent content: 0.6820 Checking the provided sequence file Detected sequence length: 270 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 540 Adjusted target solvent content: 0.54 Input MTZ file: 2h1q-4.0-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: 169 Cell parameters: 120.720 120.720 75.240 90.000 90.000 120.000 Input sequence file: 2h1q-4.0-parrot-hancs.fasta_lf Building free atoms model in initial map for 4320 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: 28.996 4.001 Wilson plot Bfac: 102.58 *** WARNING *** *** WARNING *** This resolution is too low for ARP/wARP protein chain tracing *** WARNING *** 5367 reflections ( 99.54 % complete ) and 0 restraints for refining 4764 atoms. Observations/parameters ratio is 0.28 ------------------------------------------------------ Starting model: R = 0.3522 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2867 (Rfree = 0.000) for 4764 atoms. Found 11 (22 requested) and removed 30 (11 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.98 3.77 Search for helices and strands: 0 residues in 0 chains, 4811 seeds are put forward NCS extension: 0 residues added, 4811 seeds are put forward Round 1: 117 peptides, 24 chains. Longest chain 10 peptides. Score 0.244 Round 2: 169 peptides, 32 chains. Longest chain 9 peptides. Score 0.299 Round 3: 176 peptides, 30 chains. Longest chain 15 peptides. Score 0.345 Round 4: 200 peptides, 32 chains. Longest chain 17 peptides. Score 0.386 Round 5: 189 peptides, 32 chains. Longest chain 11 peptides. Score 0.357 Taking the results from Round 4 Chains 32, Residues 168, Estimated correctness of the model 0.0 % 2 chains (6 residues) have been docked in sequence ------------------------------------------------------ 5367 reflections ( 99.54 % complete ) and 10125 restraints for refining 3894 atoms. 9473 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2717 (Rfree = 0.000) for 3894 atoms. Found 7 (18 requested) and removed 44 (9 requested) atoms. Cycle 2: After refmac, R = 0.2718 (Rfree = 0.000) for 3792 atoms. Found 11 (18 requested) and removed 30 (9 requested) atoms. Cycle 3: After refmac, R = 0.2459 (Rfree = 0.000) for 3715 atoms. Found 6 (17 requested) and removed 27 (8 requested) atoms. Cycle 4: After refmac, R = 0.2499 (Rfree = 0.000) for 3655 atoms. Found 1 (17 requested) and removed 27 (8 requested) atoms. Cycle 5: After refmac, R = 0.2363 (Rfree = 0.000) for 3603 atoms. Found 4 (17 requested) and removed 13 (8 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.96 3.75 Search for helices and strands: 0 residues in 0 chains, 3700 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 3717 seeds are put forward Round 1: 167 peptides, 35 chains. Longest chain 11 peptides. Score 0.255 Round 2: 216 peptides, 40 chains. Longest chain 12 peptides. Score 0.335 Round 3: 202 peptides, 35 chains. Longest chain 17 peptides. Score 0.356 Round 4: 226 peptides, 38 chains. Longest chain 13 peptides. Score 0.385 Round 5: 217 peptides, 34 chains. Longest chain 17 peptides. Score 0.408 Taking the results from Round 5 Chains 34, Residues 183, Estimated correctness of the model 0.0 % 2 chains (7 residues) have been docked in sequence ------------------------------------------------------ 5367 reflections ( 99.54 % complete ) and 8060 restraints for refining 3407 atoms. 7348 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2699 (Rfree = 0.000) for 3407 atoms. Found 16 (16 requested) and removed 35 (8 requested) atoms. Cycle 7: After refmac, R = 0.2309 (Rfree = 0.000) for 3353 atoms. Found 8 (16 requested) and removed 26 (8 requested) atoms. Cycle 8: After refmac, R = 0.2395 (Rfree = 0.000) for 3308 atoms. Found 6 (15 requested) and removed 12 (7 requested) atoms. Cycle 9: After refmac, R = 0.2458 (Rfree = 0.000) for 3285 atoms. Found 13 (15 requested) and removed 24 (7 requested) atoms. Cycle 10: After refmac, R = 0.2429 (Rfree = 0.000) for 3256 atoms. Found 13 (15 requested) and removed 23 (7 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.93 3.73 Search for helices and strands: 0 residues in 0 chains, 3381 seeds are put forward NCS extension: 28 residues added (1 deleted due to clashes), 3409 seeds are put forward Round 1: 175 peptides, 33 chains. Longest chain 13 peptides. Score 0.304 Round 2: 207 peptides, 35 chains. Longest chain 17 peptides. Score 0.370 Round 3: 220 peptides, 35 chains. Longest chain 15 peptides. Score 0.404 Round 4: 233 peptides, 35 chains. Longest chain 14 peptides. Score 0.437 Round 5: 231 peptides, 35 chains. Longest chain 16 peptides. Score 0.432 Taking the results from Round 4 Chains 37, Residues 198, Estimated correctness of the model 0.0 % 4 chains (25 residues) have been docked in sequence ------------------------------------------------------ 5367 reflections ( 99.54 % complete ) and 7269 restraints for refining 3316 atoms. 6459 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2374 (Rfree = 0.000) for 3316 atoms. Found 15 (15 requested) and removed 32 (7 requested) atoms. Cycle 12: After refmac, R = 0.2284 (Rfree = 0.000) for 3267 atoms. Found 6 (15 requested) and removed 24 (7 requested) atoms. Cycle 13: After refmac, R = 0.2305 (Rfree = 0.000) for 3232 atoms. Found 10 (15 requested) and removed 23 (7 requested) atoms. Cycle 14: After refmac, R = 0.2349 (Rfree = 0.000) for 3202 atoms. Found 14 (15 requested) and removed 20 (7 requested) atoms. Cycle 15: After refmac, R = 0.2326 (Rfree = 0.000) for 3185 atoms. Found 12 (15 requested) and removed 17 (7 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.95 3.74 Search for helices and strands: 0 residues in 0 chains, 3317 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 3335 seeds are put forward Round 1: 215 peptides, 43 chains. Longest chain 12 peptides. Score 0.297 Round 2: 231 peptides, 40 chains. Longest chain 16 peptides. Score 0.376 Round 3: 242 peptides, 37 chains. Longest chain 13 peptides. Score 0.437 Round 4: 243 peptides, 39 chains. Longest chain 15 peptides. Score 0.418 Round 5: 233 peptides, 37 chains. Longest chain 15 peptides. Score 0.415 Taking the results from Round 3 Chains 37, Residues 205, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 5367 reflections ( 99.54 % complete ) and 7542 restraints for refining 3336 atoms. 6745 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2594 (Rfree = 0.000) for 3336 atoms. Found 10 (15 requested) and removed 27 (7 requested) atoms. Cycle 17: After refmac, R = 0.2322 (Rfree = 0.000) for 3282 atoms. Found 15 (15 requested) and removed 20 (7 requested) atoms. Cycle 18: After refmac, R = 0.2131 (Rfree = 0.000) for 3260 atoms. Found 4 (15 requested) and removed 16 (7 requested) atoms. Cycle 19: After refmac, R = 0.2171 (Rfree = 0.000) for 3239 atoms. Found 8 (15 requested) and removed 17 (7 requested) atoms. Cycle 20: After refmac, R = 0.1914 (Rfree = 0.000) for 3226 atoms. Found 3 (15 requested) and removed 17 (7 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.94 3.74 Search for helices and strands: 0 residues in 0 chains, 3296 seeds are put forward NCS extension: 12 residues added (0 deleted due to clashes), 3308 seeds are put forward Round 1: 183 peptides, 35 chains. Longest chain 10 peptides. Score 0.302 Round 2: 205 peptides, 35 chains. Longest chain 14 peptides. Score 0.364 Round 3: 201 peptides, 34 chains. Longest chain 13 peptides. Score 0.365 Round 4: 207 peptides, 35 chains. Longest chain 14 peptides. Score 0.370 Round 5: 222 peptides, 36 chains. Longest chain 15 peptides. Score 0.398 Taking the results from Round 5 Chains 36, Residues 186, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5367 reflections ( 99.54 % complete ) and 8278 restraints for refining 3544 atoms. 7570 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2545 (Rfree = 0.000) for 3544 atoms. Found 16 (16 requested) and removed 36 (8 requested) atoms. Cycle 22: After refmac, R = 0.2291 (Rfree = 0.000) for 3494 atoms. Found 16 (16 requested) and removed 29 (8 requested) atoms. Failed to save intermediate PDB Cycle 23: After refmac, R = 0.2146 (Rfree = 0.000) for 3462 atoms. Found 16 (16 requested) and removed 18 (8 requested) atoms. Cycle 24: After refmac, R = 0.1777 (Rfree = 0.000) for 3450 atoms. Found 4 (16 requested) and removed 13 (8 requested) atoms. Cycle 25: After refmac, R = 0.1740 (Rfree = 0.000) for 3440 atoms. Found 0 (16 requested) and removed 14 (8 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.95 3.74 Search for helices and strands: 0 residues in 0 chains, 3585 seeds are put forward NCS extension: 14 residues added (2 deleted due to clashes), 3599 seeds are put forward Round 1: 172 peptides, 34 chains. Longest chain 11 peptides. Score 0.283 Round 2: 196 peptides, 33 chains. Longest chain 13 peptides. Score 0.364 Round 3: 214 peptides, 35 chains. Longest chain 12 peptides. Score 0.388 Round 4: 215 peptides, 34 chains. Longest chain 11 peptides. Score 0.403 Round 5: 229 peptides, 35 chains. Longest chain 21 peptides. Score 0.427 Taking the results from Round 5 Chains 35, Residues 194, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5367 reflections ( 99.54 % complete ) and 8412 restraints for refining 3617 atoms. 7671 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2061 (Rfree = 0.000) for 3617 atoms. Found 16 (17 requested) and removed 27 (8 requested) atoms. Cycle 27: After refmac, R = 0.2068 (Rfree = 0.000) for 3574 atoms. Found 17 (17 requested) and removed 25 (8 requested) atoms. Cycle 28: After refmac, R = 0.2007 (Rfree = 0.000) for 3545 atoms. Found 16 (16 requested) and removed 24 (8 requested) atoms. Cycle 29: After refmac, R = 0.2081 (Rfree = 0.000) for 3518 atoms. Found 16 (16 requested) and removed 25 (8 requested) atoms. Cycle 30: After refmac, R = 0.1949 (Rfree = 0.000) for 3488 atoms. Found 15 (16 requested) and removed 26 (8 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.89 3.69 Search for helices and strands: 0 residues in 0 chains, 3604 seeds are put forward NCS extension: 28 residues added (3 deleted due to clashes), 3632 seeds are put forward Round 1: 168 peptides, 36 chains. Longest chain 8 peptides. Score 0.245 Round 2: 220 peptides, 41 chains. Longest chain 13 peptides. Score 0.334 Round 3: 224 peptides, 41 chains. Longest chain 17 peptides. Score 0.345 Round 4: 222 peptides, 40 chains. Longest chain 14 peptides. Score 0.352 Round 5: 215 peptides, 40 chains. Longest chain 11 peptides. Score 0.332 Taking the results from Round 4 Chains 40, Residues 182, Estimated correctness of the model 0.0 % 2 chains (6 residues) have been docked in sequence ------------------------------------------------------ 5367 reflections ( 99.54 % complete ) and 8147 restraints for refining 3514 atoms. 7453 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2205 (Rfree = 0.000) for 3514 atoms. Found 16 (16 requested) and removed 35 (8 requested) atoms. Cycle 32: After refmac, R = 0.2074 (Rfree = 0.000) for 3466 atoms. Found 16 (16 requested) and removed 23 (8 requested) atoms. Cycle 33: After refmac, R = 0.2022 (Rfree = 0.000) for 3435 atoms. Found 16 (16 requested) and removed 16 (8 requested) atoms. Cycle 34: After refmac, R = 0.2085 (Rfree = 0.000) for 3425 atoms. Found 16 (16 requested) and removed 24 (8 requested) atoms. Cycle 35: After refmac, R = 0.1586 (Rfree = 0.000) for 3397 atoms. Found 2 (16 requested) and removed 12 (8 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.88 3.68 Search for helices and strands: 0 residues in 0 chains, 3511 seeds are put forward NCS extension: 21 residues added (2 deleted due to clashes), 3532 seeds are put forward Round 1: 150 peptides, 33 chains. Longest chain 8 peptides. Score 0.227 Round 2: 194 peptides, 37 chains. Longest chain 11 peptides. Score 0.309 Round 3: 179 peptides, 33 chains. Longest chain 9 peptides. Score 0.316 Round 4: 189 peptides, 34 chains. Longest chain 10 peptides. Score 0.332 Round 5: 184 peptides, 31 chains. Longest chain 14 peptides. Score 0.355 Taking the results from Round 5 Chains 31, Residues 153, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5367 reflections ( 99.54 % complete ) and 8322 restraints for refining 3519 atoms. 7741 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2019 (Rfree = 0.000) for 3519 atoms. Found 16 (16 requested) and removed 27 (8 requested) atoms. Cycle 37: After refmac, R = 0.1762 (Rfree = 0.000) for 3484 atoms. Found 10 (16 requested) and removed 15 (8 requested) atoms. Cycle 38: After refmac, R = 0.1753 (Rfree = 0.000) for 3469 atoms. Found 16 (16 requested) and removed 12 (8 requested) atoms. Cycle 39: After refmac, R = 0.1539 (Rfree = 0.000) for 3462 atoms. Found 3 (16 requested) and removed 11 (8 requested) atoms. Cycle 40: After refmac, R = 0.1588 (Rfree = 0.000) for 3448 atoms. Found 4 (16 requested) and removed 12 (8 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.89 3.69 Search for helices and strands: 0 residues in 0 chains, 3537 seeds are put forward NCS extension: 18 residues added (2 deleted due to clashes), 3555 seeds are put forward Round 1: 148 peptides, 31 chains. Longest chain 8 peptides. Score 0.248 Round 2: 174 peptides, 32 chains. Longest chain 9 peptides. Score 0.314 Round 3: 174 peptides, 32 chains. Longest chain 10 peptides. Score 0.314 Round 4: 180 peptides, 30 chains. Longest chain 11 peptides. Score 0.356 Round 5: 180 peptides, 33 chains. Longest chain 10 peptides. Score 0.319 Taking the results from Round 4 Chains 30, Residues 150, Estimated correctness of the model 0.0 % 3 chains (12 residues) have been docked in sequence ------------------------------------------------------ 5367 reflections ( 99.54 % complete ) and 8371 restraints for refining 3577 atoms. 7763 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2077 (Rfree = 0.000) for 3577 atoms. Found 16 (16 requested) and removed 42 (8 requested) atoms. Cycle 42: After refmac, R = 0.1864 (Rfree = 0.000) for 3531 atoms. Found 16 (16 requested) and removed 18 (8 requested) atoms. Cycle 43: After refmac, R = 0.2060 (Rfree = 0.000) for 3518 atoms. Found 16 (16 requested) and removed 22 (8 requested) atoms. Cycle 44: After refmac, R = 0.1926 (Rfree = 0.000) for 3497 atoms. Found 16 (16 requested) and removed 19 (8 requested) atoms. Cycle 45: After refmac, R = 0.1949 (Rfree = 0.000) for 3478 atoms. Found 16 (16 requested) and removed 17 (8 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.87 3.67 Search for helices and strands: 0 residues in 0 chains, 3599 seeds are put forward NCS extension: 13 residues added (0 deleted due to clashes), 3612 seeds are put forward Round 1: 158 peptides, 34 chains. Longest chain 10 peptides. Score 0.240 Round 2: 181 peptides, 34 chains. Longest chain 15 peptides. Score 0.309 Round 3: 187 peptides, 33 chains. Longest chain 14 peptides. Score 0.339 Round 4: 178 peptides, 34 chains. Longest chain 14 peptides. Score 0.300 Round 5: 193 peptides, 33 chains. Longest chain 15 peptides. Score 0.355 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 34, Residues 160, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence Sequence coverage is 5 % Consider running further cycles of model building using 2h1q-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 5367 reflections ( 99.54 % complete ) and 8422 restraints for refining 3605 atoms. 7776 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2131 (Rfree = 0.000) for 3605 atoms. Found 0 (17 requested) and removed 8 (8 requested) atoms. Cycle 47: After refmac, R = 0.1948 (Rfree = 0.000) for 3577 atoms. Found 0 (17 requested) and removed 8 (8 requested) atoms. Cycle 48: After refmac, R = 0.2043 (Rfree = 0.000) for 3552 atoms. Found 0 (16 requested) and removed 8 (8 requested) atoms. Cycle 49: After refmac, R = 0.1926 (Rfree = 0.000) for 3528 atoms. TimeTaking 59.82