Mon 24 Dec 00:49:29 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 2hi0-4.0-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2hi0-4.0-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2hi0-4.0-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2hi0-4.0-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/2hi0-4.0-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2hi0-4.0-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 00:49:34 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/2hi0-4.0-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2hi0-4.0-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 289 and 0 Target number of residues in the AU: 289 Target solvent content: 0.6639 Checking the provided sequence file Detected sequence length: 240 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 480 Adjusted target solvent content: 0.44 Input MTZ file: 2hi0-4.0-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: 58.636 38.695 103.583 90.000 98.094 90.000 Input sequence file: 2hi0-4.0-parrot-mrncs.fasta_lf Building free atoms model in initial map for 3840 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: 102.551 4.000 Wilson plot Bfac: 87.44 4096 reflections ( 99.71 % complete ) and 0 restraints for refining 4265 atoms. Observations/parameters ratio is 0.24 ------------------------------------------------------ Starting model: R = 0.3260 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2581 (Rfree = 0.000) for 4265 atoms. Found 9 (20 requested) and removed 18 (10 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.85 4.17 Search for helices and strands: 0 residues in 0 chains, 4361 seeds are put forward NCS extension: 0 residues added, 4361 seeds are put forward Round 1: 127 peptides, 29 chains. Longest chain 8 peptides. Score 0.215 Round 2: 184 peptides, 37 chains. Longest chain 8 peptides. Score 0.309 Round 3: 215 peptides, 38 chains. Longest chain 11 peptides. Score 0.404 Round 4: 226 peptides, 38 chains. Longest chain 12 peptides. Score 0.441 Round 5: 223 peptides, 36 chains. Longest chain 12 peptides. Score 0.459 Taking the results from Round 5 Chains 36, Residues 187, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4096 reflections ( 99.71 % complete ) and 8464 restraints for refining 3468 atoms. 7752 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2198 (Rfree = 0.000) for 3468 atoms. Found 16 (16 requested) and removed 22 (8 requested) atoms. Cycle 2: After refmac, R = 0.1958 (Rfree = 0.000) for 3410 atoms. Found 7 (16 requested) and removed 13 (8 requested) atoms. Cycle 3: After refmac, R = 0.1861 (Rfree = 0.000) for 3380 atoms. Found 2 (16 requested) and removed 12 (8 requested) atoms. Cycle 4: After refmac, R = 0.1853 (Rfree = 0.000) for 3351 atoms. Found 4 (16 requested) and removed 18 (8 requested) atoms. Cycle 5: After refmac, R = 0.1727 (Rfree = 0.000) for 3328 atoms. Found 2 (15 requested) and removed 12 (7 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.83 4.15 Search for helices and strands: 0 residues in 0 chains, 3444 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 3462 seeds are put forward Round 1: 179 peptides, 36 chains. Longest chain 10 peptides. Score 0.306 Round 2: 208 peptides, 35 chains. Longest chain 12 peptides. Score 0.424 Round 3: 218 peptides, 33 chains. Longest chain 14 peptides. Score 0.484 Round 4: 232 peptides, 33 chains. Longest chain 15 peptides. Score 0.526 Round 5: 220 peptides, 34 chains. Longest chain 15 peptides. Score 0.477 Taking the results from Round 4 Chains 33, Residues 199, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4096 reflections ( 99.71 % complete ) and 7911 restraints for refining 3386 atoms. 7148 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2114 (Rfree = 0.000) for 3386 atoms. Found 16 (16 requested) and removed 28 (8 requested) atoms. Cycle 7: After refmac, R = 0.1827 (Rfree = 0.000) for 3353 atoms. Found 15 (16 requested) and removed 31 (8 requested) atoms. Cycle 8: After refmac, R = 0.1946 (Rfree = 0.000) for 3325 atoms. Found 15 (15 requested) and removed 24 (7 requested) atoms. Cycle 9: After refmac, R = 0.1861 (Rfree = 0.000) for 3311 atoms. Found 15 (15 requested) and removed 22 (7 requested) atoms. Cycle 10: After refmac, R = 0.1502 (Rfree = 0.000) for 3295 atoms. Found 11 (15 requested) and removed 15 (7 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.76 4.07 Search for helices and strands: 0 residues in 0 chains, 3472 seeds are put forward NCS extension: 22 residues added (0 deleted due to clashes), 3494 seeds are put forward Round 1: 161 peptides, 34 chains. Longest chain 9 peptides. Score 0.269 Round 2: 197 peptides, 36 chains. Longest chain 13 peptides. Score 0.371 Round 3: 214 peptides, 35 chains. Longest chain 12 peptides. Score 0.444 Round 4: 225 peptides, 36 chains. Longest chain 12 peptides. Score 0.465 Round 5: 223 peptides, 35 chains. Longest chain 13 peptides. Score 0.472 Taking the results from Round 5 Chains 35, Residues 188, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4096 reflections ( 99.71 % complete ) and 8018 restraints for refining 3467 atoms. 7301 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2022 (Rfree = 0.000) for 3467 atoms. Found 16 (16 requested) and removed 28 (8 requested) atoms. Cycle 12: After refmac, R = 0.1882 (Rfree = 0.000) for 3425 atoms. Found 16 (16 requested) and removed 26 (8 requested) atoms. Cycle 13: After refmac, R = 0.1826 (Rfree = 0.000) for 3404 atoms. Found 16 (16 requested) and removed 18 (8 requested) atoms. Cycle 14: After refmac, R = 0.1709 (Rfree = 0.000) for 3391 atoms. Found 16 (16 requested) and removed 17 (8 requested) atoms. Cycle 15: After refmac, R = 0.1790 (Rfree = 0.000) for 3381 atoms. Found 16 (16 requested) and removed 17 (8 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.75 4.06 Search for helices and strands: 0 residues in 0 chains, 3548 seeds are put forward NCS extension: 13 residues added (0 deleted due to clashes), 3561 seeds are put forward Round 1: 173 peptides, 35 chains. Longest chain 12 peptides. Score 0.299 Round 2: 200 peptides, 33 chains. Longest chain 13 peptides. Score 0.426 Round 3: 184 peptides, 29 chains. Longest chain 14 peptides. Score 0.431 Round 4: 202 peptides, 32 chains. Longest chain 14 peptides. Score 0.447 Round 5: 207 peptides, 31 chains. Longest chain 13 peptides. Score 0.477 Taking the results from Round 5 Chains 31, Residues 176, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4096 reflections ( 99.71 % complete ) and 8208 restraints for refining 3445 atoms. 7535 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1864 (Rfree = 0.000) for 3445 atoms. Found 12 (16 requested) and removed 24 (8 requested) atoms. Cycle 17: After refmac, R = 0.1823 (Rfree = 0.000) for 3407 atoms. Found 16 (16 requested) and removed 17 (8 requested) atoms. Cycle 18: After refmac, R = 0.1834 (Rfree = 0.000) for 3391 atoms. Found 16 (16 requested) and removed 17 (8 requested) atoms. Cycle 19: After refmac, R = 0.1712 (Rfree = 0.000) for 3380 atoms. Found 16 (16 requested) and removed 13 (8 requested) atoms. Cycle 20: After refmac, R = 0.1389 (Rfree = 0.000) for 3373 atoms. Found 12 (16 requested) and removed 10 (8 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.73 4.04 Search for helices and strands: 0 residues in 0 chains, 3519 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 3537 seeds are put forward Round 1: 155 peptides, 30 chains. Longest chain 10 peptides. Score 0.311 Round 2: 200 peptides, 34 chains. Longest chain 11 peptides. Score 0.412 Round 3: 205 peptides, 31 chains. Longest chain 14 peptides. Score 0.471 Round 4: 212 peptides, 36 chains. Longest chain 15 peptides. Score 0.423 Round 5: 216 peptides, 33 chains. Longest chain 15 peptides. Score 0.478 Taking the results from Round 5 Chains 34, Residues 183, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 4096 reflections ( 99.71 % complete ) and 7805 restraints for refining 3449 atoms. 7076 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1756 (Rfree = 0.000) for 3449 atoms. Found 16 (16 requested) and removed 24 (8 requested) atoms. Cycle 22: After refmac, R = 0.1671 (Rfree = 0.000) for 3422 atoms. Found 16 (16 requested) and removed 14 (8 requested) atoms. Cycle 23: After refmac, R = 0.1625 (Rfree = 0.000) for 3410 atoms. Found 16 (16 requested) and removed 14 (8 requested) atoms. Cycle 24: After refmac, R = 0.1521 (Rfree = 0.000) for 3400 atoms. Found 16 (16 requested) and removed 16 (8 requested) atoms. Cycle 25: After refmac, R = 0.1511 (Rfree = 0.000) for 3395 atoms. Found 15 (16 requested) and removed 13 (8 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.71 4.02 Search for helices and strands: 0 residues in 0 chains, 3502 seeds are put forward NCS extension: 15 residues added (2 deleted due to clashes), 3517 seeds are put forward Round 1: 151 peptides, 32 chains. Longest chain 6 peptides. Score 0.263 Round 2: 177 peptides, 34 chains. Longest chain 11 peptides. Score 0.330 Round 3: 192 peptides, 32 chains. Longest chain 11 peptides. Score 0.414 Round 4: 195 peptides, 34 chains. Longest chain 11 peptides. Score 0.394 Round 5: 189 peptides, 31 chains. Longest chain 13 peptides. Score 0.418 Taking the results from Round 5 Chains 31, Residues 158, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4096 reflections ( 99.71 % complete ) and 8170 restraints for refining 3463 atoms. 7569 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1788 (Rfree = 0.000) for 3463 atoms. Found 16 (16 requested) and removed 30 (8 requested) atoms. Cycle 27: After refmac, R = 0.1711 (Rfree = 0.000) for 3429 atoms. Found 16 (16 requested) and removed 16 (8 requested) atoms. Cycle 28: After refmac, R = 0.1339 (Rfree = 0.000) for 3417 atoms. Found 6 (16 requested) and removed 15 (8 requested) atoms. Cycle 29: After refmac, R = 0.1187 (Rfree = 0.000) for 3399 atoms. Found 1 (16 requested) and removed 10 (8 requested) atoms. Cycle 30: After refmac, R = 0.1157 (Rfree = 0.000) for 3386 atoms. Found 2 (16 requested) and removed 11 (8 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.72 4.03 Search for helices and strands: 0 residues in 0 chains, 3524 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 3542 seeds are put forward Round 1: 165 peptides, 36 chains. Longest chain 9 peptides. Score 0.252 Round 2: 190 peptides, 36 chains. Longest chain 10 peptides. Score 0.347 Round 3: 186 peptides, 33 chains. Longest chain 11 peptides. Score 0.378 Round 4: 191 peptides, 32 chains. Longest chain 12 peptides. Score 0.410 Round 5: 182 peptides, 34 chains. Longest chain 11 peptides. Score 0.348 Taking the results from Round 4 Chains 32, Residues 159, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4096 reflections ( 99.71 % complete ) and 8079 restraints for refining 3440 atoms. 7475 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1761 (Rfree = 0.000) for 3440 atoms. Found 16 (16 requested) and removed 28 (8 requested) atoms. Cycle 32: After refmac, R = 0.1841 (Rfree = 0.000) for 3418 atoms. Found 16 (16 requested) and removed 20 (8 requested) atoms. Cycle 33: After refmac, R = 0.1731 (Rfree = 0.000) for 3399 atoms. Found 16 (16 requested) and removed 15 (8 requested) atoms. Cycle 34: After refmac, R = 0.1693 (Rfree = 0.000) for 3390 atoms. Found 16 (16 requested) and removed 13 (8 requested) atoms. Cycle 35: After refmac, R = 0.1313 (Rfree = 0.000) for 3381 atoms. Found 7 (16 requested) and removed 13 (8 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.70 4.01 Search for helices and strands: 0 residues in 0 chains, 3504 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 3523 seeds are put forward Round 1: 125 peptides, 28 chains. Longest chain 8 peptides. Score 0.224 Round 2: 151 peptides, 29 chains. Longest chain 9 peptides. Score 0.312 Round 3: 156 peptides, 30 chains. Longest chain 13 peptides. Score 0.315 Round 4: 171 peptides, 30 chains. Longest chain 13 peptides. Score 0.371 Round 5: 165 peptides, 31 chains. Longest chain 13 peptides. Score 0.333 Taking the results from Round 4 Chains 30, Residues 141, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4096 reflections ( 99.71 % complete ) and 7963 restraints for refining 3381 atoms. 7429 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1741 (Rfree = 0.000) for 3381 atoms. Found 16 (16 requested) and removed 22 (8 requested) atoms. Cycle 37: After refmac, R = 0.1830 (Rfree = 0.000) for 3354 atoms. Found 16 (16 requested) and removed 13 (8 requested) atoms. Cycle 38: After refmac, R = 0.1370 (Rfree = 0.000) for 3342 atoms. Found 5 (15 requested) and removed 12 (7 requested) atoms. Cycle 39: After refmac, R = 0.1288 (Rfree = 0.000) for 3326 atoms. Found 5 (15 requested) and removed 8 (7 requested) atoms. Cycle 40: After refmac, R = 0.1278 (Rfree = 0.000) for 3319 atoms. Found 5 (15 requested) and removed 8 (7 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.75 4.06 Search for helices and strands: 0 residues in 0 chains, 3437 seeds are put forward NCS extension: 8 residues added (2 deleted due to clashes), 3445 seeds are put forward Round 1: 134 peptides, 31 chains. Longest chain 6 peptides. Score 0.210 Round 2: 155 peptides, 30 chains. Longest chain 10 peptides. Score 0.311 Round 3: 160 peptides, 32 chains. Longest chain 8 peptides. Score 0.298 Round 4: 182 peptides, 33 chains. Longest chain 11 peptides. Score 0.364 Round 5: 167 peptides, 30 chains. Longest chain 8 peptides. Score 0.356 Taking the results from Round 4 Chains 33, Residues 149, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4096 reflections ( 99.71 % complete ) and 7891 restraints for refining 3375 atoms. 7328 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1664 (Rfree = 0.000) for 3375 atoms. Found 16 (16 requested) and removed 21 (8 requested) atoms. Cycle 42: After refmac, R = 0.1606 (Rfree = 0.000) for 3360 atoms. Found 16 (16 requested) and removed 15 (8 requested) atoms. Cycle 43: After refmac, R = 0.1200 (Rfree = 0.000) for 3350 atoms. Found 5 (15 requested) and removed 9 (7 requested) atoms. Cycle 44: After refmac, R = 0.1133 (Rfree = 0.000) for 3343 atoms. Found 3 (15 requested) and removed 11 (7 requested) atoms. Cycle 45: After refmac, R = 0.1132 (Rfree = 0.000) for 3334 atoms. Found 2 (15 requested) and removed 13 (7 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.71 4.02 Search for helices and strands: 0 residues in 0 chains, 3428 seeds are put forward NCS extension: 0 residues added, 3428 seeds are put forward Round 1: 124 peptides, 27 chains. Longest chain 7 peptides. Score 0.237 Round 2: 123 peptides, 22 chains. Longest chain 10 peptides. Score 0.321 Round 3: 125 peptides, 23 chains. Longest chain 12 peptides. Score 0.312 Round 4: 130 peptides, 22 chains. Longest chain 10 peptides. Score 0.348 Round 5: 121 peptides, 21 chains. Longest chain 10 peptides. Score 0.331 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 22, Residues 108, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence Sequence coverage is 0 % Consider running further cycles of model building using 2hi0-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 4096 reflections ( 99.71 % complete ) and 8140 restraints for refining 3378 atoms. 7730 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1959 (Rfree = 0.000) for 3378 atoms. Found 0 (16 requested) and removed 8 (8 requested) atoms. Cycle 47: After refmac, R = 0.2118 (Rfree = 0.000) for 3354 atoms. Found 0 (16 requested) and removed 8 (8 requested) atoms. Cycle 48: After refmac, R = 0.1878 (Rfree = 0.000) for 3334 atoms. Found 0 (15 requested) and removed 7 (7 requested) atoms. Cycle 49: After refmac, R = 0.1873 (Rfree = 0.000) for 3320 atoms. TimeTaking 37.82