Mon 24 Dec 00:33:04 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2fea-3.4-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2fea-3.4-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2fea-3.4-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2fea-3.4-parrot-mrncs 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/mrncs/ArpWArp/wArpResults/WorkingDir/2fea-3.4-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2fea-3.4-parrot-mrncs ############### 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 00:33:08 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/mrncs/ArpWArp/wArpResults/WorkingDir/2fea-3.4-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2fea-3.4-parrot-mrncs/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 377 and 0 Target number of residues in the AU: 377 Target solvent content: 0.6295 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-3.4-parrot-mrncs.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-3.4-parrot-mrncs.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 3.400 Wilson plot Bfac: 66.13 7649 reflections ( 98.32 % complete ) and 0 restraints for refining 4189 atoms. Observations/parameters ratio is 0.46 ------------------------------------------------------ Starting model: R = 0.3199 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3334 (Rfree = 0.000) for 4189 atoms. Found 31 (31 requested) and removed 148 (15 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.26 3.09 Search for helices and strands: 0 residues in 0 chains, 4140 seeds are put forward NCS extension: 0 residues added, 4140 seeds are put forward Round 1: 174 peptides, 36 chains. Longest chain 7 peptides. Score 0.273 Round 2: 226 peptides, 39 chains. Longest chain 12 peptides. Score 0.396 Round 3: 239 peptides, 40 chains. Longest chain 17 peptides. Score 0.421 Round 4: 249 peptides, 40 chains. Longest chain 13 peptides. Score 0.449 Round 5: 252 peptides, 38 chains. Longest chain 14 peptides. Score 0.481 Taking the results from Round 5 Chains 38, Residues 214, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7649 reflections ( 98.32 % complete ) and 7814 restraints for refining 3433 atoms. 6996 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3076 (Rfree = 0.000) for 3433 atoms. Found 25 (25 requested) and removed 40 (12 requested) atoms. Cycle 2: After refmac, R = 0.2777 (Rfree = 0.000) for 3369 atoms. Found 25 (25 requested) and removed 23 (12 requested) atoms. Cycle 3: After refmac, R = 0.2672 (Rfree = 0.000) for 3351 atoms. Found 25 (25 requested) and removed 27 (12 requested) atoms. Cycle 4: After refmac, R = 0.2576 (Rfree = 0.000) for 3342 atoms. Found 25 (25 requested) and removed 19 (12 requested) atoms. Cycle 5: After refmac, R = 0.2666 (Rfree = 0.000) for 3339 atoms. Found 25 (25 requested) and removed 23 (12 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.24 3.07 Search for helices and strands: 0 residues in 0 chains, 3493 seeds are put forward NCS extension: 18 residues added (3 deleted due to clashes), 3511 seeds are put forward Round 1: 226 peptides, 40 chains. Longest chain 14 peptides. Score 0.383 Round 2: 269 peptides, 46 chains. Longest chain 11 peptides. Score 0.433 Round 3: 263 peptides, 40 chains. Longest chain 15 peptides. Score 0.487 Round 4: 261 peptides, 38 chains. Longest chain 17 peptides. Score 0.504 Round 5: 276 peptides, 35 chains. Longest chain 18 peptides. Score 0.573 Taking the results from Round 5 Chains 35, Residues 241, Estimated correctness of the model 19.6 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7649 reflections ( 98.32 % complete ) and 7646 restraints for refining 3432 atoms. 6717 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2748 (Rfree = 0.000) for 3432 atoms. Found 25 (25 requested) and removed 31 (12 requested) atoms. Cycle 7: After refmac, R = 0.2618 (Rfree = 0.000) for 3408 atoms. Found 25 (25 requested) and removed 21 (12 requested) atoms. Cycle 8: After refmac, R = 0.2447 (Rfree = 0.000) for 3398 atoms. Found 25 (25 requested) and removed 22 (12 requested) atoms. Cycle 9: After refmac, R = 0.2472 (Rfree = 0.000) for 3393 atoms. Found 25 (25 requested) and removed 20 (12 requested) atoms. Cycle 10: After refmac, R = 0.2319 (Rfree = 0.000) for 3388 atoms. Found 25 (25 requested) and removed 19 (12 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.24 3.07 Search for helices and strands: 0 residues in 0 chains, 3568 seeds are put forward NCS extension: 0 residues added, 3568 seeds are put forward Round 1: 223 peptides, 39 chains. Longest chain 11 peptides. Score 0.387 Round 2: 255 peptides, 39 chains. Longest chain 14 peptides. Score 0.477 Round 3: 251 peptides, 39 chains. Longest chain 13 peptides. Score 0.466 Round 4: 250 peptides, 36 chains. Longest chain 14 peptides. Score 0.499 Round 5: 274 peptides, 35 chains. Longest chain 19 peptides. Score 0.568 Taking the results from Round 5 Chains 36, Residues 239, Estimated correctness of the model 17.9 % 1 chains (13 residues) have been docked in sequence ------------------------------------------------------ 7649 reflections ( 98.32 % complete ) and 7531 restraints for refining 3433 atoms. 6552 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2394 (Rfree = 0.000) for 3433 atoms. Found 25 (25 requested) and removed 21 (12 requested) atoms. Cycle 12: After refmac, R = 0.2364 (Rfree = 0.000) for 3417 atoms. Found 25 (25 requested) and removed 18 (12 requested) atoms. Cycle 13: After refmac, R = 0.2202 (Rfree = 0.000) for 3416 atoms. Found 14 (25 requested) and removed 17 (12 requested) atoms. Cycle 14: After refmac, R = 0.1957 (Rfree = 0.000) for 3405 atoms. Found 7 (25 requested) and removed 16 (12 requested) atoms. Cycle 15: After refmac, R = 0.1932 (Rfree = 0.000) for 3392 atoms. Found 3 (25 requested) and removed 14 (12 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.24 3.07 Search for helices and strands: 0 residues in 0 chains, 3507 seeds are put forward NCS extension: 24 residues added (1 deleted due to clashes), 3531 seeds are put forward Round 1: 231 peptides, 42 chains. Longest chain 12 peptides. Score 0.373 Round 2: 249 peptides, 36 chains. Longest chain 21 peptides. Score 0.496 Round 3: 249 peptides, 34 chains. Longest chain 16 peptides. Score 0.519 Round 4: 236 peptides, 32 chains. Longest chain 14 peptides. Score 0.509 Round 5: 257 peptides, 41 chains. Longest chain 15 peptides. Score 0.459 Taking the results from Round 3 Chains 34, Residues 215, Estimated correctness of the model 0.0 % 2 chains (7 residues) have been docked in sequence ------------------------------------------------------ 7649 reflections ( 98.32 % complete ) and 7798 restraints for refining 3433 atoms. 6957 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2289 (Rfree = 0.000) for 3433 atoms. Found 19 (25 requested) and removed 25 (12 requested) atoms. Cycle 17: After refmac, R = 0.2100 (Rfree = 0.000) for 3416 atoms. Found 25 (25 requested) and removed 13 (12 requested) atoms. Cycle 18: After refmac, R = 0.2044 (Rfree = 0.000) for 3420 atoms. Found 13 (25 requested) and removed 15 (12 requested) atoms. Cycle 19: After refmac, R = 0.1952 (Rfree = 0.000) for 3412 atoms. Found 11 (25 requested) and removed 12 (12 requested) atoms. Cycle 20: After refmac, R = 0.1959 (Rfree = 0.000) for 3406 atoms. Found 17 (25 requested) and removed 14 (12 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.28 3.11 Search for helices and strands: 0 residues in 0 chains, 3550 seeds are put forward NCS extension: 16 residues added (2 deleted due to clashes), 3566 seeds are put forward Round 1: 231 peptides, 40 chains. Longest chain 14 peptides. Score 0.398 Round 2: 262 peptides, 36 chains. Longest chain 22 peptides. Score 0.529 Round 3: 251 peptides, 38 chains. Longest chain 18 peptides. Score 0.478 Round 4: 261 peptides, 40 chains. Longest chain 15 peptides. Score 0.481 Round 5: 261 peptides, 36 chains. Longest chain 17 peptides. Score 0.526 Taking the results from Round 2 Chains 36, Residues 226, Estimated correctness of the model 3.8 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7649 reflections ( 98.32 % complete ) and 7620 restraints for refining 3433 atoms. 6752 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2127 (Rfree = 0.000) for 3433 atoms. Found 18 (25 requested) and removed 14 (12 requested) atoms. Cycle 22: After refmac, R = 0.2003 (Rfree = 0.000) for 3429 atoms. Found 11 (25 requested) and removed 12 (12 requested) atoms. Cycle 23: After refmac, R = 0.1976 (Rfree = 0.000) for 3425 atoms. Found 18 (25 requested) and removed 15 (12 requested) atoms. Cycle 24: After refmac, R = 0.1912 (Rfree = 0.000) for 3424 atoms. Found 13 (25 requested) and removed 12 (12 requested) atoms. Cycle 25: After refmac, R = 0.1894 (Rfree = 0.000) for 3422 atoms. Found 15 (25 requested) and removed 14 (12 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.25 3.08 Search for helices and strands: 0 residues in 0 chains, 3548 seeds are put forward NCS extension: 30 residues added (2 deleted due to clashes), 3578 seeds are put forward Round 1: 219 peptides, 37 chains. Longest chain 16 peptides. Score 0.401 Round 2: 234 peptides, 33 chains. Longest chain 16 peptides. Score 0.492 Round 3: 247 peptides, 37 chains. Longest chain 15 peptides. Score 0.479 Round 4: 241 peptides, 37 chains. Longest chain 14 peptides. Score 0.463 Round 5: 240 peptides, 36 chains. Longest chain 35 peptides. Score 0.472 Taking the results from Round 2 Chains 33, Residues 201, Estimated correctness of the model 0.0 % 1 chains (14 residues) have been docked in sequence ------------------------------------------------------ 7649 reflections ( 98.32 % complete ) and 7575 restraints for refining 3432 atoms. 6742 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2152 (Rfree = 0.000) for 3432 atoms. Found 18 (25 requested) and removed 15 (12 requested) atoms. Cycle 27: After refmac, R = 0.2068 (Rfree = 0.000) for 3422 atoms. Found 19 (25 requested) and removed 12 (12 requested) atoms. Cycle 28: After refmac, R = 0.2001 (Rfree = 0.000) for 3425 atoms. Found 16 (25 requested) and removed 14 (12 requested) atoms. Cycle 29: After refmac, R = 0.1935 (Rfree = 0.000) for 3424 atoms. Found 11 (25 requested) and removed 14 (12 requested) atoms. Cycle 30: After refmac, R = 0.1847 (Rfree = 0.000) for 3418 atoms. Found 12 (25 requested) and removed 13 (12 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.25 3.08 Search for helices and strands: 0 residues in 0 chains, 3553 seeds are put forward NCS extension: 18 residues added (2 deleted due to clashes), 3571 seeds are put forward Round 1: 207 peptides, 36 chains. Longest chain 13 peptides. Score 0.378 Round 2: 245 peptides, 39 chains. Longest chain 16 peptides. Score 0.450 Round 3: 239 peptides, 34 chains. Longest chain 17 peptides. Score 0.493 Round 4: 237 peptides, 34 chains. Longest chain 17 peptides. Score 0.488 Round 5: 219 peptides, 27 chains. Longest chain 17 peptides. Score 0.523 Taking the results from Round 5 Chains 27, Residues 192, Estimated correctness of the model 1.6 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ 7649 reflections ( 98.32 % complete ) and 7769 restraints for refining 3433 atoms. 7001 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2161 (Rfree = 0.000) for 3433 atoms. Found 25 (25 requested) and removed 18 (12 requested) atoms. Cycle 32: After refmac, R = 0.2054 (Rfree = 0.000) for 3431 atoms. Found 24 (25 requested) and removed 16 (12 requested) atoms. Cycle 33: After refmac, R = 0.1999 (Rfree = 0.000) for 3435 atoms. Found 21 (25 requested) and removed 16 (12 requested) atoms. Cycle 34: After refmac, R = 0.2010 (Rfree = 0.000) for 3436 atoms. Found 22 (25 requested) and removed 13 (12 requested) atoms. Cycle 35: After refmac, R = 0.1908 (Rfree = 0.000) for 3443 atoms. Found 16 (26 requested) and removed 15 (13 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.25 3.08 Search for helices and strands: 0 residues in 0 chains, 3556 seeds are put forward NCS extension: 18 residues added (2 deleted due to clashes), 3574 seeds are put forward Round 1: 193 peptides, 34 chains. Longest chain 13 peptides. Score 0.362 Round 2: 221 peptides, 32 chains. Longest chain 18 peptides. Score 0.469 Round 3: 211 peptides, 33 chains. Longest chain 11 peptides. Score 0.429 Round 4: 222 peptides, 32 chains. Longest chain 19 peptides. Score 0.472 Round 5: 222 peptides, 32 chains. Longest chain 14 peptides. Score 0.472 Taking the results from Round 5 Chains 32, Residues 190, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7649 reflections ( 98.32 % complete ) and 7924 restraints for refining 3432 atoms. 7196 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2222 (Rfree = 0.000) for 3432 atoms. Found 19 (25 requested) and removed 13 (12 requested) atoms. Cycle 37: After refmac, R = 0.2008 (Rfree = 0.000) for 3426 atoms. Found 13 (25 requested) and removed 12 (12 requested) atoms. Cycle 38: After refmac, R = 0.1926 (Rfree = 0.000) for 3419 atoms. Found 12 (25 requested) and removed 16 (12 requested) atoms. Cycle 39: After refmac, R = 0.1860 (Rfree = 0.000) for 3410 atoms. Found 16 (25 requested) and removed 15 (12 requested) atoms. Cycle 40: After refmac, R = 0.1818 (Rfree = 0.000) for 3409 atoms. Found 9 (25 requested) and removed 14 (12 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.27 3.10 Search for helices and strands: 0 residues in 0 chains, 3541 seeds are put forward NCS extension: 0 residues added, 3541 seeds are put forward Round 1: 189 peptides, 39 chains. Longest chain 10 peptides. Score 0.281 Round 2: 210 peptides, 33 chains. Longest chain 17 peptides. Score 0.426 Round 3: 204 peptides, 35 chains. Longest chain 14 peptides. Score 0.382 Round 4: 225 peptides, 35 chains. Longest chain 12 peptides. Score 0.443 Round 5: 221 peptides, 36 chains. Longest chain 11 peptides. Score 0.419 Taking the results from Round 4 Chains 35, Residues 190, Estimated correctness of the model 0.0 % 1 chains (11 residues) have been docked in sequence ------------------------------------------------------ 7649 reflections ( 98.32 % complete ) and 7699 restraints for refining 3433 atoms. 6938 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2090 (Rfree = 0.000) for 3433 atoms. Found 20 (25 requested) and removed 16 (12 requested) atoms. Cycle 42: After refmac, R = 0.1983 (Rfree = 0.000) for 3419 atoms. Found 20 (25 requested) and removed 16 (12 requested) atoms. Cycle 43: After refmac, R = 0.1918 (Rfree = 0.000) for 3414 atoms. Found 14 (25 requested) and removed 12 (12 requested) atoms. Cycle 44: After refmac, R = 0.1853 (Rfree = 0.000) for 3410 atoms. Found 12 (25 requested) and removed 14 (12 requested) atoms. Cycle 45: After refmac, R = 0.1899 (Rfree = 0.000) for 3402 atoms. Found 14 (25 requested) and removed 14 (12 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.24 3.07 Search for helices and strands: 0 residues in 0 chains, 3518 seeds are put forward NCS extension: 13 residues added (0 deleted due to clashes), 3531 seeds are put forward Round 1: 168 peptides, 32 chains. Longest chain 9 peptides. Score 0.310 Round 2: 176 peptides, 30 chains. Longest chain 11 peptides. Score 0.363 Round 3: 192 peptides, 32 chains. Longest chain 11 peptides. Score 0.385 Round 4: 195 peptides, 30 chains. Longest chain 11 peptides. Score 0.421 Round 5: 174 peptides, 32 chains. Longest chain 10 peptides. Score 0.329 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 30, Residues 165, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence Sequence coverage is 6 % Consider running further cycles of model building using 2fea-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 7649 reflections ( 98.32 % complete ) and 7937 restraints for refining 3433 atoms. 7272 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2098 (Rfree = 0.000) for 3433 atoms. Found 0 (25 requested) and removed 12 (12 requested) atoms. Cycle 47: After refmac, R = 0.2084 (Rfree = 0.000) for 3409 atoms. Found 0 (25 requested) and removed 12 (12 requested) atoms. Cycle 48: After refmac, R = 0.2000 (Rfree = 0.000) for 3391 atoms. Found 0 (25 requested) and removed 12 (12 requested) atoms. Cycle 49: After refmac, R = 0.1930 (Rfree = 0.000) for 3374 atoms. TimeTaking 36.43