Mon 24 Dec 07:29:54 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 2fea-3.2-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2fea-3.2-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2fea-3.2-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2fea-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/2fea-3.2-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2fea-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 07:29:58 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/2fea-3.2-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2fea-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 390 and 0 Target number of residues in the AU: 390 Target solvent content: 0.6168 Checking the provided sequence file Detected sequence length: 236 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 472 Adjusted target solvent content: 0.54 Input MTZ file: 2fea-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: 4 Cell parameters: 59.005 43.112 109.575 90.000 98.912 90.000 Input sequence file: 2fea-3.2-parrot-noncs.fasta_lf Building free atoms model in initial map for 3776 target number of atoms Had to go as low as 0.65 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: 22.949 3.200 Wilson plot Bfac: 59.58 9144 reflections ( 98.33 % complete ) and 0 restraints for refining 4188 atoms. Observations/parameters ratio is 0.55 ------------------------------------------------------ Starting model: R = 0.3207 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2628 (Rfree = 0.000) for 4188 atoms. Found 37 (37 requested) and removed 46 (18 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.05 2.89 Search for helices and strands: 0 residues in 0 chains, 4276 seeds are put forward NCS extension: 0 residues added, 4276 seeds are put forward Round 1: 236 peptides, 45 chains. Longest chain 11 peptides. Score 0.350 Round 2: 273 peptides, 43 chains. Longest chain 15 peptides. Score 0.479 Round 3: 307 peptides, 45 chains. Longest chain 14 peptides. Score 0.542 Round 4: 279 peptides, 40 chains. Longest chain 15 peptides. Score 0.527 Round 5: 307 peptides, 42 chains. Longest chain 19 peptides. Score 0.572 Taking the results from Round 5 Chains 42, Residues 265, Estimated correctness of the model 33.3 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 9144 reflections ( 98.33 % complete ) and 7458 restraints for refining 3447 atoms. 6440 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2498 (Rfree = 0.000) for 3447 atoms. Found 28 (30 requested) and removed 25 (15 requested) atoms. Cycle 2: After refmac, R = 0.2314 (Rfree = 0.000) for 3428 atoms. Found 9 (30 requested) and removed 19 (15 requested) atoms. Cycle 3: After refmac, R = 0.2290 (Rfree = 0.000) for 3408 atoms. Found 5 (30 requested) and removed 17 (15 requested) atoms. Cycle 4: After refmac, R = 0.2274 (Rfree = 0.000) for 3391 atoms. Found 7 (30 requested) and removed 16 (15 requested) atoms. Cycle 5: After refmac, R = 0.2269 (Rfree = 0.000) for 3379 atoms. Found 6 (30 requested) and removed 15 (15 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.08 2.92 Search for helices and strands: 0 residues in 0 chains, 3512 seeds are put forward NCS extension: 19 residues added (3 deleted due to clashes), 3531 seeds are put forward Round 1: 283 peptides, 47 chains. Longest chain 15 peptides. Score 0.459 Round 2: 292 peptides, 40 chains. Longest chain 16 peptides. Score 0.558 Round 3: 295 peptides, 35 chains. Longest chain 24 peptides. Score 0.615 Round 4: 292 peptides, 40 chains. Longest chain 27 peptides. Score 0.558 Round 5: 281 peptides, 37 chains. Longest chain 23 peptides. Score 0.564 Taking the results from Round 3 Chains 35, Residues 260, Estimated correctness of the model 45.0 % 2 chains (11 residues) have been docked in sequence ------------------------------------------------------ 9144 reflections ( 98.33 % complete ) and 7573 restraints for refining 3447 atoms. 6541 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2425 (Rfree = 0.000) for 3447 atoms. Found 26 (30 requested) and removed 22 (15 requested) atoms. Cycle 7: After refmac, R = 0.2248 (Rfree = 0.000) for 3440 atoms. Found 6 (30 requested) and removed 17 (15 requested) atoms. Cycle 8: After refmac, R = 0.2215 (Rfree = 0.000) for 3420 atoms. Found 12 (30 requested) and removed 17 (15 requested) atoms. Cycle 9: After refmac, R = 0.2146 (Rfree = 0.000) for 3409 atoms. Found 6 (30 requested) and removed 16 (15 requested) atoms. Cycle 10: After refmac, R = 0.2099 (Rfree = 0.000) for 3396 atoms. Found 4 (30 requested) and removed 15 (15 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.13 2.97 Search for helices and strands: 0 residues in 0 chains, 3486 seeds are put forward NCS extension: 26 residues added (3 deleted due to clashes), 3512 seeds are put forward Round 1: 272 peptides, 40 chains. Longest chain 23 peptides. Score 0.510 Round 2: 307 peptides, 39 chains. Longest chain 24 peptides. Score 0.602 Round 3: 291 peptides, 36 chains. Longest chain 20 peptides. Score 0.597 Round 4: 301 peptides, 37 chains. Longest chain 16 peptides. Score 0.608 Round 5: 297 peptides, 37 chains. Longest chain 19 peptides. Score 0.600 Taking the results from Round 4 Chains 37, Residues 264, Estimated correctness of the model 43.2 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 9144 reflections ( 98.33 % complete ) and 7785 restraints for refining 3445 atoms. 6766 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2375 (Rfree = 0.000) for 3445 atoms. Found 30 (30 requested) and removed 16 (15 requested) atoms. Cycle 12: After refmac, R = 0.2166 (Rfree = 0.000) for 3449 atoms. Found 13 (31 requested) and removed 16 (15 requested) atoms. Cycle 13: After refmac, R = 0.2086 (Rfree = 0.000) for 3439 atoms. Found 8 (30 requested) and removed 15 (15 requested) atoms. Cycle 14: After refmac, R = 0.2045 (Rfree = 0.000) for 3426 atoms. Found 3 (30 requested) and removed 15 (15 requested) atoms. Cycle 15: After refmac, R = 0.2017 (Rfree = 0.000) for 3412 atoms. Found 1 (30 requested) and removed 15 (15 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.14 2.98 Search for helices and strands: 0 residues in 0 chains, 3495 seeds are put forward NCS extension: 16 residues added (2 deleted due to clashes), 3511 seeds are put forward Round 1: 272 peptides, 40 chains. Longest chain 29 peptides. Score 0.510 Round 2: 296 peptides, 34 chains. Longest chain 19 peptides. Score 0.626 Round 3: 296 peptides, 38 chains. Longest chain 20 peptides. Score 0.588 Round 4: 295 peptides, 35 chains. Longest chain 27 peptides. Score 0.615 Round 5: 282 peptides, 35 chains. Longest chain 22 peptides. Score 0.587 Taking the results from Round 2 Chains 35, Residues 262, Estimated correctness of the model 47.9 % 3 chains (31 residues) have been docked in sequence ------------------------------------------------------ 9144 reflections ( 98.33 % complete ) and 7365 restraints for refining 3447 atoms. 6248 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2345 (Rfree = 0.000) for 3447 atoms. Found 28 (30 requested) and removed 24 (15 requested) atoms. Cycle 17: After refmac, R = 0.2156 (Rfree = 0.000) for 3445 atoms. Found 15 (30 requested) and removed 16 (15 requested) atoms. Cycle 18: After refmac, R = 0.2118 (Rfree = 0.000) for 3441 atoms. Found 7 (30 requested) and removed 15 (15 requested) atoms. Cycle 19: After refmac, R = 0.2091 (Rfree = 0.000) for 3429 atoms. Found 8 (30 requested) and removed 16 (15 requested) atoms. Cycle 20: After refmac, R = 0.2078 (Rfree = 0.000) for 3419 atoms. Found 7 (30 requested) and removed 15 (15 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.14 2.98 Search for helices and strands: 0 residues in 0 chains, 3514 seeds are put forward NCS extension: 27 residues added (0 deleted due to clashes), 3541 seeds are put forward Round 1: 258 peptides, 37 chains. Longest chain 17 peptides. Score 0.508 Round 2: 295 peptides, 40 chains. Longest chain 19 peptides. Score 0.565 Round 3: 297 peptides, 37 chains. Longest chain 19 peptides. Score 0.600 Round 4: 299 peptides, 37 chains. Longest chain 23 peptides. Score 0.604 Round 5: 303 peptides, 37 chains. Longest chain 26 peptides. Score 0.613 Taking the results from Round 5 Chains 38, Residues 266, Estimated correctness of the model 44.5 % 1 chains (11 residues) have been docked in sequence ------------------------------------------------------ 9144 reflections ( 98.33 % complete ) and 7428 restraints for refining 3447 atoms. 6352 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2383 (Rfree = 0.000) for 3447 atoms. Found 27 (30 requested) and removed 16 (15 requested) atoms. Cycle 22: After refmac, R = 0.2187 (Rfree = 0.000) for 3449 atoms. Found 9 (31 requested) and removed 16 (15 requested) atoms. Cycle 23: After refmac, R = 0.2122 (Rfree = 0.000) for 3440 atoms. Found 14 (30 requested) and removed 15 (15 requested) atoms. Cycle 24: After refmac, R = 0.2088 (Rfree = 0.000) for 3438 atoms. Found 4 (30 requested) and removed 15 (15 requested) atoms. Cycle 25: After refmac, R = 0.2066 (Rfree = 0.000) for 3424 atoms. Found 4 (30 requested) and removed 15 (15 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.14 2.98 Search for helices and strands: 0 residues in 0 chains, 3528 seeds are put forward NCS extension: 31 residues added (3 deleted due to clashes), 3559 seeds are put forward Round 1: 262 peptides, 39 chains. Longest chain 28 peptides. Score 0.495 Round 2: 279 peptides, 36 chains. Longest chain 19 peptides. Score 0.570 Round 3: 286 peptides, 34 chains. Longest chain 30 peptides. Score 0.605 Round 4: 287 peptides, 32 chains. Longest chain 45 peptides. Score 0.627 Round 5: 298 peptides, 37 chains. Longest chain 25 peptides. Score 0.602 Taking the results from Round 4 Chains 32, Residues 255, Estimated correctness of the model 48.1 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 9144 reflections ( 98.33 % complete ) and 7737 restraints for refining 3447 atoms. 6749 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2328 (Rfree = 0.000) for 3447 atoms. Found 20 (30 requested) and removed 17 (15 requested) atoms. Cycle 27: After refmac, R = 0.2209 (Rfree = 0.000) for 3447 atoms. Found 11 (30 requested) and removed 16 (15 requested) atoms. Cycle 28: After refmac, R = 0.2134 (Rfree = 0.000) for 3439 atoms. Found 8 (30 requested) and removed 15 (15 requested) atoms. Cycle 29: After refmac, R = 0.2085 (Rfree = 0.000) for 3432 atoms. Found 2 (30 requested) and removed 15 (15 requested) atoms. Cycle 30: After refmac, R = 0.2059 (Rfree = 0.000) for 3419 atoms. Found 8 (30 requested) and removed 15 (15 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.14 2.98 Search for helices and strands: 0 residues in 0 chains, 3516 seeds are put forward NCS extension: 38 residues added (8 deleted due to clashes), 3554 seeds are put forward Round 1: 261 peptides, 40 chains. Longest chain 21 peptides. Score 0.481 Round 2: 274 peptides, 32 chains. Longest chain 21 peptides. Score 0.599 Round 3: 276 peptides, 36 chains. Longest chain 22 peptides. Score 0.563 Round 4: 264 peptides, 37 chains. Longest chain 18 peptides. Score 0.523 Round 5: 280 peptides, 37 chains. Longest chain 16 peptides. Score 0.561 Taking the results from Round 2 Chains 32, Residues 242, Estimated correctness of the model 40.8 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 9144 reflections ( 98.33 % complete ) and 7822 restraints for refining 3447 atoms. 6886 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2230 (Rfree = 0.000) for 3447 atoms. Found 18 (30 requested) and removed 16 (15 requested) atoms. Cycle 32: After refmac, R = 0.2120 (Rfree = 0.000) for 3445 atoms. Found 7 (30 requested) and removed 15 (15 requested) atoms. Cycle 33: After refmac, R = 0.2081 (Rfree = 0.000) for 3436 atoms. Found 3 (30 requested) and removed 15 (15 requested) atoms. Cycle 34: After refmac, R = 0.2081 (Rfree = 0.000) for 3421 atoms. Found 4 (30 requested) and removed 15 (15 requested) atoms. Cycle 35: After refmac, R = 0.2058 (Rfree = 0.000) for 3410 atoms. Found 10 (30 requested) and removed 15 (15 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.14 2.98 Search for helices and strands: 0 residues in 0 chains, 3529 seeds are put forward NCS extension: 24 residues added (1 deleted due to clashes), 3553 seeds are put forward Round 1: 235 peptides, 40 chains. Longest chain 14 peptides. Score 0.410 Round 2: 256 peptides, 29 chains. Longest chain 28 peptides. Score 0.590 Round 3: 253 peptides, 33 chains. Longest chain 28 peptides. Score 0.540 Round 4: 244 peptides, 28 chains. Longest chain 36 peptides. Score 0.573 Round 5: 244 peptides, 34 chains. Longest chain 15 peptides. Score 0.506 Taking the results from Round 2 Chains 30, Residues 227, Estimated correctness of the model 38.3 % 1 chains (25 residues) have been docked in sequence ------------------------------------------------------ 9144 reflections ( 98.33 % complete ) and 7514 restraints for refining 3447 atoms. 6514 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2346 (Rfree = 0.000) for 3447 atoms. Found 22 (30 requested) and removed 22 (15 requested) atoms. Cycle 37: After refmac, R = 0.2346 (Rfree = 0.000) for 3445 atoms. Found 11 (30 requested) and removed 15 (15 requested) atoms. Cycle 38: After refmac, R = 0.2092 (Rfree = 0.000) for 3438 atoms. Found 4 (30 requested) and removed 16 (15 requested) atoms. Cycle 39: After refmac, R = 0.2127 (Rfree = 0.000) for 3424 atoms. Found 1 (30 requested) and removed 15 (15 requested) atoms. Cycle 40: After refmac, R = 0.2033 (Rfree = 0.000) for 3410 atoms. Found 5 (30 requested) and removed 15 (15 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.14 2.98 Search for helices and strands: 0 residues in 0 chains, 3496 seeds are put forward NCS extension: 23 residues added (0 deleted due to clashes), 3519 seeds are put forward Round 1: 242 peptides, 38 chains. Longest chain 14 peptides. Score 0.454 Round 2: 273 peptides, 37 chains. Longest chain 21 peptides. Score 0.545 Round 3: 277 peptides, 36 chains. Longest chain 22 peptides. Score 0.565 Round 4: 268 peptides, 35 chains. Longest chain 20 peptides. Score 0.554 Round 5: 275 peptides, 35 chains. Longest chain 18 peptides. Score 0.571 Taking the results from Round 5 Chains 35, Residues 240, Estimated correctness of the model 33.0 % 1 chains (15 residues) have been docked in sequence ------------------------------------------------------ 9144 reflections ( 98.33 % complete ) and 7527 restraints for refining 3447 atoms. 6537 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2383 (Rfree = 0.000) for 3447 atoms. Found 24 (30 requested) and removed 17 (15 requested) atoms. Cycle 42: After refmac, R = 0.2286 (Rfree = 0.000) for 3452 atoms. Found 9 (30 requested) and removed 15 (15 requested) atoms. Cycle 43: After refmac, R = 0.2171 (Rfree = 0.000) for 3440 atoms. Found 9 (30 requested) and removed 16 (15 requested) atoms. Cycle 44: After refmac, R = 0.2133 (Rfree = 0.000) for 3428 atoms. Found 7 (30 requested) and removed 15 (15 requested) atoms. Cycle 45: After refmac, R = 0.2069 (Rfree = 0.000) for 3419 atoms. Found 4 (30 requested) and removed 15 (15 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.15 2.99 Search for helices and strands: 0 residues in 0 chains, 3522 seeds are put forward NCS extension: 13 residues added (1 deleted due to clashes), 3535 seeds are put forward Round 1: 234 peptides, 38 chains. Longest chain 16 peptides. Score 0.432 Round 2: 284 peptides, 36 chains. Longest chain 21 peptides. Score 0.581 Round 3: 272 peptides, 35 chains. Longest chain 19 peptides. Score 0.564 Round 4: 261 peptides, 33 chains. Longest chain 24 peptides. Score 0.559 Round 5: 258 peptides, 34 chains. Longest chain 23 peptides. Score 0.541 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 36, Residues 248, Estimated correctness of the model 35.8 % 1 chains (20 residues) have been docked in sequence Sequence coverage is 8 % Consider running further cycles of model building using 2fea-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 9144 reflections ( 98.33 % complete ) and 7325 restraints for refining 3446 atoms. 6286 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2379 (Rfree = 0.000) for 3446 atoms. Found 0 (30 requested) and removed 11 (15 requested) atoms. Cycle 47: After refmac, R = 0.2149 (Rfree = 0.000) for 3432 atoms. Found 0 (30 requested) and removed 3 (15 requested) atoms. Cycle 48: After refmac, R = 0.2111 (Rfree = 0.000) for 3429 atoms. Found 0 (30 requested) and removed 3 (15 requested) atoms. Cycle 49: After refmac, R = 0.2112 (Rfree = 0.000) for 3421 atoms. TimeTaking 40.3