Mon 24 Dec 00:21:00 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 2hi0-3.8-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2hi0-3.8-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2hi0-3.8-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2hi0-3.8-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/2hi0-3.8-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2hi0-3.8-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 00:21:04 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/2hi0-3.8-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2hi0-3.8-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 301 and 0 Target number of residues in the AU: 301 Target solvent content: 0.6499 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: 2hi0-3.8-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: 2hi0-3.8-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 3.800 Wilson plot Bfac: 78.00 4764 reflections ( 99.75 % complete ) and 0 restraints for refining 4234 atoms. Observations/parameters ratio is 0.28 ------------------------------------------------------ Starting model: R = 0.3253 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2972 (Rfree = 0.000) for 4234 atoms. Found 20 (23 requested) and removed 25 (11 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.55 3.85 Search for helices and strands: 0 residues in 0 chains, 4330 seeds are put forward NCS extension: 0 residues added, 4330 seeds are put forward Round 1: 155 peptides, 32 chains. Longest chain 7 peptides. Score 0.278 Round 2: 223 peptides, 40 chains. Longest chain 13 peptides. Score 0.402 Round 3: 253 peptides, 40 chains. Longest chain 16 peptides. Score 0.498 Round 4: 271 peptides, 45 chains. Longest chain 13 peptides. Score 0.487 Round 5: 256 peptides, 39 chains. Longest chain 14 peptides. Score 0.519 Taking the results from Round 5 Chains 39, Residues 217, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4764 reflections ( 99.75 % complete ) and 8006 restraints for refining 3472 atoms. 7177 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2313 (Rfree = 0.000) for 3472 atoms. Found 11 (19 requested) and removed 20 (9 requested) atoms. Cycle 2: After refmac, R = 0.2073 (Rfree = 0.000) for 3408 atoms. Found 12 (19 requested) and removed 21 (9 requested) atoms. Cycle 3: After refmac, R = 0.1743 (Rfree = 0.000) for 3378 atoms. Found 7 (18 requested) and removed 11 (9 requested) atoms. Cycle 4: After refmac, R = 0.1594 (Rfree = 0.000) for 3366 atoms. Found 5 (18 requested) and removed 12 (9 requested) atoms. Cycle 5: After refmac, R = 0.1580 (Rfree = 0.000) for 3358 atoms. Found 5 (18 requested) and removed 18 (9 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.58 3.88 Search for helices and strands: 0 residues in 0 chains, 3471 seeds are put forward NCS extension: 11 residues added (3 deleted due to clashes), 3482 seeds are put forward Round 1: 220 peptides, 40 chains. Longest chain 10 peptides. Score 0.392 Round 2: 241 peptides, 40 chains. Longest chain 12 peptides. Score 0.461 Round 3: 241 peptides, 40 chains. Longest chain 11 peptides. Score 0.461 Round 4: 258 peptides, 41 chains. Longest chain 14 peptides. Score 0.500 Round 5: 257 peptides, 42 chains. Longest chain 13 peptides. Score 0.484 Taking the results from Round 4 Chains 41, Residues 217, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 4764 reflections ( 99.75 % complete ) and 7731 restraints for refining 3400 atoms. 6874 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 6: After refmac, R = 0.1991 (Rfree = 0.000) for 3400 atoms. Found 16 (18 requested) and removed 15 (9 requested) atoms. Cycle 7: After refmac, R = 0.1759 (Rfree = 0.000) for 3380 atoms. Found 17 (18 requested) and removed 12 (9 requested) atoms. Cycle 8: After refmac, R = 0.1885 (Rfree = 0.000) for 3373 atoms. Found 14 (18 requested) and removed 13 (9 requested) atoms. Cycle 9: After refmac, R = 0.1676 (Rfree = 0.000) for 3363 atoms. Found 12 (18 requested) and removed 15 (9 requested) atoms. Cycle 10: After refmac, R = 0.1748 (Rfree = 0.000) for 3351 atoms. Found 15 (18 requested) and removed 15 (9 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.57 3.87 Search for helices and strands: 0 residues in 0 chains, 3479 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 3493 seeds are put forward Round 1: 216 peptides, 45 chains. Longest chain 8 peptides. Score 0.304 Round 2: 233 peptides, 37 chains. Longest chain 13 peptides. Score 0.477 Round 3: 224 peptides, 35 chains. Longest chain 13 peptides. Score 0.476 Round 4: 233 peptides, 33 chains. Longest chain 13 peptides. Score 0.529 Round 5: 241 peptides, 40 chains. Longest chain 15 peptides. Score 0.461 Taking the results from Round 4 Chains 33, Residues 200, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4764 reflections ( 99.75 % complete ) and 8018 restraints for refining 3474 atoms. 7251 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2079 (Rfree = 0.000) for 3474 atoms. Found 19 (19 requested) and removed 18 (9 requested) atoms. Cycle 12: After refmac, R = 0.1791 (Rfree = 0.000) for 3450 atoms. Found 11 (19 requested) and removed 14 (9 requested) atoms. Cycle 13: After refmac, R = 0.1712 (Rfree = 0.000) for 3431 atoms. Found 14 (18 requested) and removed 14 (9 requested) atoms. Cycle 14: After refmac, R = 0.1668 (Rfree = 0.000) for 3425 atoms. Found 15 (18 requested) and removed 12 (9 requested) atoms. Cycle 15: After refmac, R = 0.1329 (Rfree = 0.000) for 3419 atoms. Found 5 (18 requested) and removed 11 (9 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.56 3.86 Search for helices and strands: 0 residues in 0 chains, 3545 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 3560 seeds are put forward Round 1: 215 peptides, 44 chains. Longest chain 9 peptides. Score 0.316 Round 2: 245 peptides, 45 chains. Longest chain 11 peptides. Score 0.405 Round 3: 249 peptides, 44 chains. Longest chain 11 peptides. Score 0.432 Round 4: 248 peptides, 41 chains. Longest chain 14 peptides. Score 0.470 Round 5: 255 peptides, 39 chains. Longest chain 16 peptides. Score 0.517 Taking the results from Round 5 Chains 39, Residues 216, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 4764 reflections ( 99.75 % complete ) and 8005 restraints for refining 3474 atoms. 7160 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1834 (Rfree = 0.000) for 3474 atoms. Found 19 (19 requested) and removed 18 (9 requested) atoms. Cycle 17: After refmac, R = 0.1684 (Rfree = 0.000) for 3456 atoms. Found 19 (19 requested) and removed 16 (9 requested) atoms. Cycle 18: After refmac, R = 0.1711 (Rfree = 0.000) for 3448 atoms. Found 19 (19 requested) and removed 17 (9 requested) atoms. Cycle 19: After refmac, R = 0.1663 (Rfree = 0.000) for 3443 atoms. Found 18 (18 requested) and removed 14 (9 requested) atoms. Cycle 20: After refmac, R = 0.1708 (Rfree = 0.000) for 3443 atoms. Found 18 (18 requested) and removed 13 (9 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.58 3.88 Search for helices and strands: 0 residues in 0 chains, 3584 seeds are put forward NCS extension: 20 residues added (0 deleted due to clashes), 3604 seeds are put forward Round 1: 175 peptides, 39 chains. Longest chain 8 peptides. Score 0.243 Round 2: 199 peptides, 36 chains. Longest chain 13 peptides. Score 0.379 Round 3: 211 peptides, 37 chains. Longest chain 11 peptides. Score 0.405 Round 4: 219 peptides, 39 chains. Longest chain 11 peptides. Score 0.403 Round 5: 239 peptides, 38 chains. Longest chain 16 peptides. Score 0.482 Taking the results from Round 5 Chains 39, Residues 201, Estimated correctness of the model 0.0 % 2 chains (21 residues) have been docked in sequence ------------------------------------------------------ 4764 reflections ( 99.75 % complete ) and 7939 restraints for refining 3474 atoms. 7096 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1924 (Rfree = 0.000) for 3474 atoms. Found 19 (19 requested) and removed 18 (9 requested) atoms. Cycle 22: After refmac, R = 0.1614 (Rfree = 0.000) for 3466 atoms. Found 17 (19 requested) and removed 17 (9 requested) atoms. Cycle 23: After refmac, R = 0.1531 (Rfree = 0.000) for 3459 atoms. Found 15 (19 requested) and removed 14 (9 requested) atoms. Cycle 24: After refmac, R = 0.1514 (Rfree = 0.000) for 3455 atoms. Found 19 (19 requested) and removed 11 (9 requested) atoms. Cycle 25: After refmac, R = 0.1562 (Rfree = 0.000) for 3459 atoms. Found 19 (19 requested) and removed 14 (9 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.54 3.84 Search for helices and strands: 0 residues in 0 chains, 3586 seeds are put forward NCS extension: 19 residues added (1 deleted due to clashes), 3605 seeds are put forward Round 1: 181 peptides, 38 chains. Longest chain 10 peptides. Score 0.282 Round 2: 205 peptides, 38 chains. Longest chain 11 peptides. Score 0.370 Round 3: 192 peptides, 33 chains. Longest chain 12 peptides. Score 0.399 Round 4: 201 peptides, 35 chains. Longest chain 11 peptides. Score 0.400 Round 5: 185 peptides, 34 chains. Longest chain 9 peptides. Score 0.359 Taking the results from Round 4 Chains 35, Residues 166, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4764 reflections ( 99.75 % complete ) and 8296 restraints for refining 3474 atoms. 7667 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1640 (Rfree = 0.000) for 3474 atoms. Found 16 (19 requested) and removed 13 (9 requested) atoms. Cycle 27: After refmac, R = 0.1717 (Rfree = 0.000) for 3462 atoms. Found 19 (19 requested) and removed 11 (9 requested) atoms. Cycle 28: After refmac, R = 0.1686 (Rfree = 0.000) for 3460 atoms. Found 19 (19 requested) and removed 15 (9 requested) atoms. Cycle 29: After refmac, R = 0.1234 (Rfree = 0.000) for 3452 atoms. Found 8 (19 requested) and removed 11 (9 requested) atoms. Cycle 30: After refmac, R = 0.1348 (Rfree = 0.000) for 3442 atoms. Found 18 (18 requested) and removed 11 (9 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.55 3.85 Search for helices and strands: 0 residues in 0 chains, 3589 seeds are put forward NCS extension: 12 residues added (0 deleted due to clashes), 3601 seeds are put forward Round 1: 171 peptides, 39 chains. Longest chain 6 peptides. Score 0.227 Round 2: 194 peptides, 35 chains. Longest chain 13 peptides. Score 0.376 Round 3: 198 peptides, 35 chains. Longest chain 11 peptides. Score 0.390 Round 4: 199 peptides, 37 chains. Longest chain 10 peptides. Score 0.364 Round 5: 199 peptides, 34 chains. Longest chain 11 peptides. Score 0.408 Taking the results from Round 5 Chains 34, Residues 165, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4764 reflections ( 99.75 % complete ) and 8189 restraints for refining 3472 atoms. 7563 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1771 (Rfree = 0.000) for 3472 atoms. Found 14 (19 requested) and removed 13 (9 requested) atoms. Cycle 32: After refmac, R = 0.1656 (Rfree = 0.000) for 3457 atoms. Found 19 (19 requested) and removed 14 (9 requested) atoms. Cycle 33: After refmac, R = 0.1622 (Rfree = 0.000) for 3453 atoms. Found 19 (19 requested) and removed 18 (9 requested) atoms. Cycle 34: After refmac, R = 0.1520 (Rfree = 0.000) for 3447 atoms. Found 18 (18 requested) and removed 17 (9 requested) atoms. Cycle 35: After refmac, R = 0.1593 (Rfree = 0.000) for 3443 atoms. Found 18 (18 requested) and removed 13 (9 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.58 3.88 Search for helices and strands: 0 residues in 0 chains, 3556 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 3570 seeds are put forward Round 1: 127 peptides, 27 chains. Longest chain 9 peptides. Score 0.250 Round 2: 167 peptides, 31 chains. Longest chain 14 peptides. Score 0.340 Round 3: 197 peptides, 37 chains. Longest chain 13 peptides. Score 0.356 Round 4: 191 peptides, 33 chains. Longest chain 14 peptides. Score 0.396 Round 5: 196 peptides, 38 chains. Longest chain 9 peptides. Score 0.338 Taking the results from Round 4 Chains 33, Residues 158, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4764 reflections ( 99.75 % complete ) and 8257 restraints for refining 3449 atoms. 7658 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1756 (Rfree = 0.000) for 3449 atoms. Found 18 (18 requested) and removed 28 (9 requested) atoms. Cycle 37: After refmac, R = 0.1525 (Rfree = 0.000) for 3428 atoms. Found 18 (18 requested) and removed 19 (9 requested) atoms. Cycle 38: After refmac, R = 0.1504 (Rfree = 0.000) for 3420 atoms. Found 18 (18 requested) and removed 22 (9 requested) atoms. Cycle 39: After refmac, R = 0.1165 (Rfree = 0.000) for 3410 atoms. Found 9 (18 requested) and removed 10 (9 requested) atoms. Cycle 40: After refmac, R = 0.1227 (Rfree = 0.000) for 3404 atoms. Found 6 (18 requested) and removed 11 (9 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.58 3.88 Search for helices and strands: 0 residues in 0 chains, 3493 seeds are put forward NCS extension: 23 residues added (1 deleted due to clashes), 3516 seeds are put forward Round 1: 142 peptides, 31 chains. Longest chain 9 peptides. Score 0.243 Round 2: 162 peptides, 32 chains. Longest chain 10 peptides. Score 0.305 Round 3: 172 peptides, 33 chains. Longest chain 10 peptides. Score 0.327 Round 4: 180 peptides, 32 chains. Longest chain 11 peptides. Score 0.372 Round 5: 184 peptides, 33 chains. Longest chain 10 peptides. Score 0.371 Taking the results from Round 4 Chains 32, Residues 148, Estimated correctness of the model 0.0 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ 4764 reflections ( 99.75 % complete ) and 8266 restraints for refining 3473 atoms. 7687 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1670 (Rfree = 0.000) for 3473 atoms. Found 19 (19 requested) and removed 25 (9 requested) atoms. Cycle 42: After refmac, R = 0.1657 (Rfree = 0.000) for 3456 atoms. Found 19 (19 requested) and removed 14 (9 requested) atoms. Cycle 43: After refmac, R = 0.1463 (Rfree = 0.000) for 3455 atoms. Found 15 (19 requested) and removed 21 (9 requested) atoms. Cycle 44: After refmac, R = 0.1644 (Rfree = 0.000) for 3445 atoms. Found 18 (18 requested) and removed 15 (9 requested) atoms. Cycle 45: After refmac, R = 0.1477 (Rfree = 0.000) for 3443 atoms. Found 18 (18 requested) and removed 12 (9 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.57 3.87 Search for helices and strands: 0 residues in 0 chains, 3545 seeds are put forward NCS extension: 0 residues added, 3545 seeds are put forward Round 1: 135 peptides, 30 chains. Longest chain 9 peptides. Score 0.231 Round 2: 166 peptides, 33 chains. Longest chain 10 peptides. Score 0.305 Round 3: 184 peptides, 33 chains. Longest chain 11 peptides. Score 0.371 Round 4: 159 peptides, 30 chains. Longest chain 14 peptides. Score 0.326 Round 5: 173 peptides, 29 chains. Longest chain 11 peptides. Score 0.393 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 29, Residues 144, 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 2hi0-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 4764 reflections ( 99.75 % complete ) and 8289 restraints for refining 3473 atoms. 7702 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1657 (Rfree = 0.000) for 3473 atoms. Found 0 (19 requested) and removed 9 (9 requested) atoms. Cycle 47: After refmac, R = 0.1576 (Rfree = 0.000) for 3452 atoms. Found 0 (19 requested) and removed 9 (9 requested) atoms. Cycle 48: After refmac, R = 0.1630 (Rfree = 0.000) for 3438 atoms. Found 0 (18 requested) and removed 9 (9 requested) atoms. Cycle 49: After refmac, R = 0.1485 (Rfree = 0.000) for 3423 atoms. Found 0 (18 requested) and removed 9 (9 requested) atoms. Writing output files ... TimeTaking 36.83