Mon 24 Dec 01:08:23 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 2hi0-3.6-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2hi0-3.6-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2hi0-3.6-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2hi0-3.6-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/2hi0-3.6-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2hi0-3.6-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 01:08:28 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/2hi0-3.6-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2hi0-3.6-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 313 and 0 Target number of residues in the AU: 313 Target solvent content: 0.6360 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: 2hi0-3.6-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: 2hi0-3.6-parrot-mrncs.fasta_lf Building free atoms model in initial map for 3840 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: 102.551 3.600 Wilson plot Bfac: 69.72 5572 reflections ( 99.77 % complete ) and 0 restraints for refining 4266 atoms. Observations/parameters ratio is 0.33 ------------------------------------------------------ Starting model: R = 0.3143 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2879 (Rfree = 0.000) for 4266 atoms. Found 27 (27 requested) and removed 26 (13 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.38 3.66 Search for helices and strands: 0 residues in 0 chains, 4368 seeds are put forward NCS extension: 0 residues added, 4368 seeds are put forward Round 1: 170 peptides, 39 chains. Longest chain 7 peptides. Score 0.223 Round 2: 223 peptides, 42 chains. Longest chain 10 peptides. Score 0.374 Round 3: 240 peptides, 40 chains. Longest chain 11 peptides. Score 0.458 Round 4: 226 peptides, 37 chains. Longest chain 13 peptides. Score 0.455 Round 5: 244 peptides, 36 chains. Longest chain 14 peptides. Score 0.523 Taking the results from Round 5 Chains 36, Residues 208, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5572 reflections ( 99.77 % complete ) and 7915 restraints for refining 3480 atoms. 7119 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2234 (Rfree = 0.000) for 3480 atoms. Found 18 (22 requested) and removed 28 (11 requested) atoms. Cycle 2: After refmac, R = 0.2146 (Rfree = 0.000) for 3421 atoms. Found 20 (22 requested) and removed 16 (11 requested) atoms. Cycle 3: After refmac, R = 0.1883 (Rfree = 0.000) for 3413 atoms. Found 10 (21 requested) and removed 15 (10 requested) atoms. Cycle 4: After refmac, R = 0.1796 (Rfree = 0.000) for 3393 atoms. Found 11 (21 requested) and removed 12 (10 requested) atoms. Cycle 5: After refmac, R = 0.1739 (Rfree = 0.000) for 3383 atoms. Found 7 (21 requested) and removed 11 (10 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.36 3.64 Search for helices and strands: 0 residues in 0 chains, 3528 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 3545 seeds are put forward Round 1: 212 peptides, 38 chains. Longest chain 10 peptides. Score 0.394 Round 2: 249 peptides, 41 chains. Longest chain 15 peptides. Score 0.473 Round 3: 261 peptides, 40 chains. Longest chain 13 peptides. Score 0.521 Round 4: 259 peptides, 40 chains. Longest chain 11 peptides. Score 0.516 Round 5: 264 peptides, 35 chains. Longest chain 21 peptides. Score 0.590 Taking the results from Round 5 Chains 36, Residues 229, Estimated correctness of the model 10.7 % 2 chains (19 residues) have been docked in sequence ------------------------------------------------------ 5572 reflections ( 99.77 % complete ) and 7687 restraints for refining 3479 atoms. 6736 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2066 (Rfree = 0.000) for 3479 atoms. Found 13 (22 requested) and removed 20 (11 requested) atoms. Cycle 7: After refmac, R = 0.1932 (Rfree = 0.000) for 3439 atoms. Found 12 (22 requested) and removed 17 (11 requested) atoms. Cycle 8: After refmac, R = 0.1861 (Rfree = 0.000) for 3425 atoms. Found 7 (22 requested) and removed 14 (11 requested) atoms. Cycle 9: After refmac, R = 0.1886 (Rfree = 0.000) for 3414 atoms. Found 6 (21 requested) and removed 12 (10 requested) atoms. Cycle 10: After refmac, R = 0.1808 (Rfree = 0.000) for 3403 atoms. Found 8 (21 requested) and removed 14 (10 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.43 3.72 Search for helices and strands: 0 residues in 0 chains, 3514 seeds are put forward NCS extension: 22 residues added (0 deleted due to clashes), 3536 seeds are put forward Round 1: 220 peptides, 41 chains. Longest chain 10 peptides. Score 0.378 Round 2: 250 peptides, 38 chains. Longest chain 18 peptides. Score 0.515 Round 3: 263 peptides, 41 chains. Longest chain 14 peptides. Score 0.515 Round 4: 265 peptides, 40 chains. Longest chain 15 peptides. Score 0.533 Round 5: 263 peptides, 40 chains. Longest chain 17 peptides. Score 0.527 Taking the results from Round 4 Chains 41, Residues 225, Estimated correctness of the model 0.0 % 2 chains (18 residues) have been docked in sequence ------------------------------------------------------ 5572 reflections ( 99.77 % complete ) and 7845 restraints for refining 3481 atoms. 6926 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2097 (Rfree = 0.000) for 3481 atoms. Found 22 (22 requested) and removed 17 (11 requested) atoms. Cycle 12: After refmac, R = 0.1981 (Rfree = 0.000) for 3470 atoms. Found 7 (22 requested) and removed 16 (11 requested) atoms. Cycle 13: After refmac, R = 0.1855 (Rfree = 0.000) for 3453 atoms. Found 8 (22 requested) and removed 16 (11 requested) atoms. Cycle 14: After refmac, R = 0.1760 (Rfree = 0.000) for 3442 atoms. Found 6 (22 requested) and removed 13 (11 requested) atoms. Cycle 15: After refmac, R = 0.1700 (Rfree = 0.000) for 3428 atoms. Found 7 (22 requested) and removed 13 (11 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.42 3.71 Search for helices and strands: 0 residues in 0 chains, 3558 seeds are put forward NCS extension: 0 residues added, 3558 seeds are put forward Round 1: 207 peptides, 41 chains. Longest chain 8 peptides. Score 0.332 Round 2: 244 peptides, 38 chains. Longest chain 17 peptides. Score 0.497 Round 3: 242 peptides, 38 chains. Longest chain 15 peptides. Score 0.491 Round 4: 256 peptides, 37 chains. Longest chain 12 peptides. Score 0.544 Round 5: 252 peptides, 33 chains. Longest chain 18 peptides. Score 0.582 Taking the results from Round 5 Chains 33, Residues 219, Estimated correctness of the model 7.5 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5572 reflections ( 99.77 % complete ) and 8044 restraints for refining 3481 atoms. 7201 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2004 (Rfree = 0.000) for 3481 atoms. Found 13 (22 requested) and removed 15 (11 requested) atoms. Cycle 17: After refmac, R = 0.1826 (Rfree = 0.000) for 3471 atoms. Found 16 (22 requested) and removed 15 (11 requested) atoms. Cycle 18: After refmac, R = 0.1692 (Rfree = 0.000) for 3469 atoms. Found 18 (22 requested) and removed 17 (11 requested) atoms. Cycle 19: After refmac, R = 0.1616 (Rfree = 0.000) for 3468 atoms. Found 15 (22 requested) and removed 18 (11 requested) atoms. Cycle 20: After refmac, R = 0.1614 (Rfree = 0.000) for 3463 atoms. Found 12 (22 requested) and removed 18 (11 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.37 3.65 Search for helices and strands: 0 residues in 0 chains, 3610 seeds are put forward NCS extension: 21 residues added (1 deleted due to clashes), 3631 seeds are put forward Round 1: 201 peptides, 41 chains. Longest chain 11 peptides. Score 0.310 Round 2: 238 peptides, 35 chains. Longest chain 19 peptides. Score 0.518 Round 3: 223 peptides, 36 chains. Longest chain 14 peptides. Score 0.459 Round 4: 225 peptides, 34 chains. Longest chain 18 peptides. Score 0.492 Round 5: 244 peptides, 38 chains. Longest chain 13 peptides. Score 0.497 Taking the results from Round 2 Chains 36, Residues 203, Estimated correctness of the model 0.0 % 1 chains (11 residues) have been docked in sequence ------------------------------------------------------ 5572 reflections ( 99.77 % complete ) and 7891 restraints for refining 3481 atoms. 7078 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1756 (Rfree = 0.000) for 3481 atoms. Found 17 (22 requested) and removed 16 (11 requested) atoms. Cycle 22: After refmac, R = 0.1602 (Rfree = 0.000) for 3475 atoms. Found 8 (22 requested) and removed 13 (11 requested) atoms. Cycle 23: After refmac, R = 0.1580 (Rfree = 0.000) for 3467 atoms. Found 8 (22 requested) and removed 15 (11 requested) atoms. Cycle 24: After refmac, R = 0.1522 (Rfree = 0.000) for 3458 atoms. Found 6 (22 requested) and removed 12 (11 requested) atoms. Cycle 25: After refmac, R = 0.1493 (Rfree = 0.000) for 3452 atoms. Found 7 (22 requested) and removed 13 (11 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.34 3.62 Search for helices and strands: 0 residues in 0 chains, 3576 seeds are put forward NCS extension: 13 residues added (1 deleted due to clashes), 3589 seeds are put forward Round 1: 187 peptides, 37 chains. Longest chain 9 peptides. Score 0.320 Round 2: 210 peptides, 36 chains. Longest chain 12 peptides. Score 0.416 Round 3: 209 peptides, 36 chains. Longest chain 11 peptides. Score 0.413 Round 4: 217 peptides, 36 chains. Longest chain 11 peptides. Score 0.439 Round 5: 199 peptides, 31 chains. Longest chain 14 peptides. Score 0.452 Taking the results from Round 5 Chains 31, Residues 168, Estimated correctness of the model 0.0 % 1 chains (13 residues) have been docked in sequence ------------------------------------------------------ 5572 reflections ( 99.77 % complete ) and 8110 restraints for refining 3481 atoms. 7412 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1811 (Rfree = 0.000) for 3481 atoms. Found 17 (22 requested) and removed 17 (11 requested) atoms. Cycle 27: After refmac, R = 0.1697 (Rfree = 0.000) for 3468 atoms. Found 8 (22 requested) and removed 14 (11 requested) atoms. Cycle 28: After refmac, R = 0.1634 (Rfree = 0.000) for 3449 atoms. Found 9 (22 requested) and removed 13 (11 requested) atoms. Cycle 29: After refmac, R = 0.1558 (Rfree = 0.000) for 3436 atoms. Found 6 (22 requested) and removed 17 (11 requested) atoms. Cycle 30: After refmac, R = 0.1559 (Rfree = 0.000) for 3421 atoms. Found 7 (21 requested) and removed 11 (10 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.36 3.64 Search for helices and strands: 0 residues in 0 chains, 3516 seeds are put forward NCS extension: 0 residues added, 3516 seeds are put forward Round 1: 185 peptides, 38 chains. Longest chain 10 peptides. Score 0.297 Round 2: 222 peptides, 38 chains. Longest chain 12 peptides. Score 0.428 Round 3: 207 peptides, 33 chains. Longest chain 18 peptides. Score 0.449 Round 4: 214 peptides, 34 chains. Longest chain 14 peptides. Score 0.458 Round 5: 221 peptides, 33 chains. Longest chain 19 peptides. Score 0.493 Taking the results from Round 5 Chains 34, Residues 188, Estimated correctness of the model 0.0 % 1 chains (11 residues) have been docked in sequence ------------------------------------------------------ 5572 reflections ( 99.77 % complete ) and 7980 restraints for refining 3480 atoms. 7216 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1876 (Rfree = 0.000) for 3480 atoms. Found 22 (22 requested) and removed 13 (11 requested) atoms. Cycle 32: After refmac, R = 0.1643 (Rfree = 0.000) for 3484 atoms. Found 11 (22 requested) and removed 13 (11 requested) atoms. Cycle 33: After refmac, R = 0.1557 (Rfree = 0.000) for 3479 atoms. Found 4 (22 requested) and removed 11 (11 requested) atoms. Cycle 34: After refmac, R = 0.1528 (Rfree = 0.000) for 3471 atoms. Found 8 (22 requested) and removed 11 (11 requested) atoms. Cycle 35: After refmac, R = 0.1509 (Rfree = 0.000) for 3465 atoms. Found 3 (22 requested) and removed 11 (11 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.37 3.65 Search for helices and strands: 0 residues in 0 chains, 3569 seeds are put forward NCS extension: 20 residues added (2 deleted due to clashes), 3589 seeds are put forward Round 1: 175 peptides, 34 chains. Longest chain 13 peptides. Score 0.323 Round 2: 206 peptides, 38 chains. Longest chain 14 peptides. Score 0.373 Round 3: 191 peptides, 35 chains. Longest chain 14 peptides. Score 0.365 Round 4: 191 peptides, 34 chains. Longest chain 16 peptides. Score 0.380 Round 5: 181 peptides, 30 chains. Longest chain 16 peptides. Score 0.406 Taking the results from Round 5 Chains 30, Residues 151, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5572 reflections ( 99.77 % complete ) and 8356 restraints for refining 3480 atoms. 7782 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1682 (Rfree = 0.000) for 3480 atoms. Found 14 (22 requested) and removed 15 (11 requested) atoms. Cycle 37: After refmac, R = 0.1568 (Rfree = 0.000) for 3472 atoms. Found 7 (22 requested) and removed 11 (11 requested) atoms. Cycle 38: After refmac, R = 0.1522 (Rfree = 0.000) for 3467 atoms. Found 0 (22 requested) and removed 11 (11 requested) atoms. Cycle 39: After refmac, R = 0.1517 (Rfree = 0.000) for 3454 atoms. Found 5 (22 requested) and removed 11 (11 requested) atoms. Cycle 40: After refmac, R = 0.1493 (Rfree = 0.000) for 3448 atoms. Found 2 (22 requested) and removed 11 (11 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.39 3.67 Search for helices and strands: 0 residues in 0 chains, 3537 seeds are put forward NCS extension: 0 residues added, 3537 seeds are put forward Round 1: 176 peptides, 35 chains. Longest chain 11 peptides. Score 0.311 Round 2: 187 peptides, 33 chains. Longest chain 11 peptides. Score 0.382 Round 3: 192 peptides, 33 chains. Longest chain 18 peptides. Score 0.399 Round 4: 193 peptides, 33 chains. Longest chain 15 peptides. Score 0.402 Round 5: 192 peptides, 33 chains. Longest chain 12 peptides. Score 0.399 Taking the results from Round 4 Chains 33, Residues 160, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5572 reflections ( 99.77 % complete ) and 8315 restraints for refining 3481 atoms. 7708 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1779 (Rfree = 0.000) for 3481 atoms. Found 13 (22 requested) and removed 12 (11 requested) atoms. Cycle 42: After refmac, R = 0.1712 (Rfree = 0.000) for 3475 atoms. Found 7 (22 requested) and removed 11 (11 requested) atoms. Cycle 43: After refmac, R = 0.1666 (Rfree = 0.000) for 3469 atoms. Found 9 (22 requested) and removed 13 (11 requested) atoms. Cycle 44: After refmac, R = 0.1622 (Rfree = 0.000) for 3462 atoms. Found 5 (22 requested) and removed 12 (11 requested) atoms. Cycle 45: After refmac, R = 0.1638 (Rfree = 0.000) for 3451 atoms. Found 9 (22 requested) and removed 13 (11 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.38 3.66 Search for helices and strands: 0 residues in 0 chains, 3565 seeds are put forward NCS extension: 21 residues added (1 deleted due to clashes), 3586 seeds are put forward Round 1: 158 peptides, 34 chains. Longest chain 11 peptides. Score 0.257 Round 2: 169 peptides, 33 chains. Longest chain 10 peptides. Score 0.316 Round 3: 178 peptides, 34 chains. Longest chain 10 peptides. Score 0.334 Round 4: 167 peptides, 32 chains. Longest chain 11 peptides. Score 0.324 Round 5: 173 peptides, 33 chains. Longest chain 8 peptides. Score 0.331 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 34, Residues 144, 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 2hi0-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 5572 reflections ( 99.77 % complete ) and 8408 restraints for refining 3480 atoms. 7866 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1725 (Rfree = 0.000) for 3480 atoms. Found 0 (22 requested) and removed 11 (11 requested) atoms. Cycle 47: After refmac, R = 0.1659 (Rfree = 0.000) for 3459 atoms. Found 0 (22 requested) and removed 11 (11 requested) atoms. Cycle 48: After refmac, R = 0.1735 (Rfree = 0.000) for 3446 atoms. Found 0 (22 requested) and removed 5 (11 requested) atoms. Cycle 49: After refmac, R = 0.1735 (Rfree = 0.000) for 3439 atoms. TimeTaking 42.7