null Mon 24 Dec 01:09:01 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 2hi0-3.2-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2hi0-3.2-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2hi0-3.2-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2hi0-3.2-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/2hi0-3.2-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2hi0-3.2-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 01:09:06 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/2hi0-3.2-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2hi0-3.2-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 334 and 0 Target number of residues in the AU: 334 Target solvent content: 0.6116 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: 2hi0-3.2-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: 2hi0-3.2-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 3.200 Wilson plot Bfac: 57.25 7883 reflections ( 99.82 % complete ) and 0 restraints for refining 4273 atoms. Observations/parameters ratio is 0.46 ------------------------------------------------------ Starting model: R = 0.3048 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2685 (Rfree = 0.000) for 4273 atoms. Found 38 (38 requested) and removed 42 (19 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.12 3.38 Search for helices and strands: 0 residues in 0 chains, 4355 seeds are put forward NCS extension: 0 residues added, 4355 seeds are put forward Round 1: 220 peptides, 45 chains. Longest chain 12 peptides. Score 0.319 Round 2: 280 peptides, 42 chains. Longest chain 17 peptides. Score 0.550 Round 3: 290 peptides, 42 chains. Longest chain 20 peptides. Score 0.577 Round 4: 293 peptides, 41 chains. Longest chain 19 peptides. Score 0.596 Round 5: 312 peptides, 43 chains. Longest chain 18 peptides. Score 0.621 Taking the results from Round 5 Chains 43, Residues 269, Estimated correctness of the model 46.6 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7883 reflections ( 99.82 % complete ) and 7739 restraints for refining 3501 atoms. 6706 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2426 (Rfree = 0.000) for 3501 atoms. Found 31 (31 requested) and removed 27 (15 requested) atoms. Cycle 2: After refmac, R = 0.2220 (Rfree = 0.000) for 3458 atoms. Found 14 (31 requested) and removed 20 (15 requested) atoms. Cycle 3: After refmac, R = 0.2182 (Rfree = 0.000) for 3431 atoms. Found 14 (30 requested) and removed 17 (15 requested) atoms. Cycle 4: After refmac, R = 0.2112 (Rfree = 0.000) for 3415 atoms. Found 15 (30 requested) and removed 17 (15 requested) atoms. Cycle 5: After refmac, R = 0.2055 (Rfree = 0.000) for 3403 atoms. Found 14 (30 requested) and removed 20 (15 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.06 3.32 Search for helices and strands: 0 residues in 0 chains, 3518 seeds are put forward NCS extension: 17 residues added (2 deleted due to clashes), 3535 seeds are put forward Round 1: 272 peptides, 40 chains. Longest chain 15 peptides. Score 0.552 Round 2: 304 peptides, 33 chains. Longest chain 23 peptides. Score 0.702 Round 3: 306 peptides, 30 chains. Longest chain 24 peptides. Score 0.732 Round 4: 327 peptides, 37 chains. Longest chain 25 peptides. Score 0.710 Round 5: 340 peptides, 38 chains. Longest chain 25 peptides. Score 0.726 Taking the results from Round 3 Chains 35, Residues 276, Estimated correctness of the model 71.7 % 3 chains (39 residues) have been docked in sequence Building loops using Loopy2018 35 chains (276 residues) following loop building 3 chains (39 residues) in sequence following loop building ------------------------------------------------------ 7883 reflections ( 99.82 % complete ) and 7354 restraints for refining 3496 atoms. 6124 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2263 (Rfree = 0.000) for 3496 atoms. Found 24 (31 requested) and removed 25 (15 requested) atoms. Cycle 7: After refmac, R = 0.2110 (Rfree = 0.000) for 3486 atoms. Found 14 (30 requested) and removed 20 (15 requested) atoms. Cycle 8: After refmac, R = 0.2105 (Rfree = 0.000) for 3468 atoms. Found 8 (30 requested) and removed 16 (15 requested) atoms. Cycle 9: After refmac, R = 0.2051 (Rfree = 0.000) for 3457 atoms. Found 7 (29 requested) and removed 20 (15 requested) atoms. Cycle 10: After refmac, R = 0.2041 (Rfree = 0.000) for 3439 atoms. Found 12 (28 requested) and removed 18 (15 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.07 3.33 Search for helices and strands: 0 residues in 0 chains, 3564 seeds are put forward NCS extension: 27 residues added (5 deleted due to clashes), 3591 seeds are put forward Round 1: 270 peptides, 41 chains. Longest chain 15 peptides. Score 0.535 Round 2: 297 peptides, 33 chains. Longest chain 25 peptides. Score 0.687 Round 3: 302 peptides, 41 chains. Longest chain 17 peptides. Score 0.618 Round 4: 296 peptides, 35 chains. Longest chain 25 peptides. Score 0.666 Round 5: 302 peptides, 40 chains. Longest chain 16 peptides. Score 0.629 Taking the results from Round 2 Chains 36, Residues 264, Estimated correctness of the model 62.4 % 3 chains (29 residues) have been docked in sequence ------------------------------------------------------ 7883 reflections ( 99.82 % complete ) and 7518 restraints for refining 3506 atoms. 6403 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2116 (Rfree = 0.000) for 3506 atoms. Found 21 (28 requested) and removed 19 (15 requested) atoms. Cycle 12: After refmac, R = 0.2050 (Rfree = 0.000) for 3506 atoms. Found 14 (28 requested) and removed 15 (15 requested) atoms. Cycle 13: After refmac, R = 0.2028 (Rfree = 0.000) for 3499 atoms. Found 14 (28 requested) and removed 16 (15 requested) atoms. Cycle 14: After refmac, R = 0.1962 (Rfree = 0.000) for 3494 atoms. Found 10 (28 requested) and removed 15 (15 requested) atoms. Cycle 15: After refmac, R = 0.1979 (Rfree = 0.000) for 3485 atoms. Found 12 (28 requested) and removed 15 (15 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.09 3.35 Search for helices and strands: 0 residues in 0 chains, 3595 seeds are put forward NCS extension: 31 residues added (2 deleted due to clashes), 3626 seeds are put forward Round 1: 275 peptides, 42 chains. Longest chain 24 peptides. Score 0.537 Round 2: 293 peptides, 38 chains. Longest chain 21 peptides. Score 0.629 Round 3: 302 peptides, 42 chains. Longest chain 22 peptides. Score 0.608 Round 4: 304 peptides, 37 chains. Longest chain 22 peptides. Score 0.664 Round 5: 310 peptides, 41 chains. Longest chain 16 peptides. Score 0.637 Taking the results from Round 4 Chains 37, Residues 267, Estimated correctness of the model 57.2 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7883 reflections ( 99.82 % complete ) and 7818 restraints for refining 3506 atoms. 6787 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2115 (Rfree = 0.000) for 3506 atoms. Found 20 (28 requested) and removed 18 (15 requested) atoms. Cycle 17: After refmac, R = 0.2030 (Rfree = 0.000) for 3502 atoms. Found 12 (28 requested) and removed 16 (15 requested) atoms. Cycle 18: After refmac, R = 0.1987 (Rfree = 0.000) for 3497 atoms. Found 12 (28 requested) and removed 18 (15 requested) atoms. Cycle 19: After refmac, R = 0.1945 (Rfree = 0.000) for 3489 atoms. Found 12 (28 requested) and removed 15 (15 requested) atoms. Cycle 20: After refmac, R = 0.1930 (Rfree = 0.000) for 3484 atoms. Found 13 (28 requested) and removed 18 (15 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.09 3.35 Search for helices and strands: 0 residues in 0 chains, 3584 seeds are put forward NCS extension: 24 residues added (3 deleted due to clashes), 3608 seeds are put forward Round 1: 255 peptides, 40 chains. Longest chain 17 peptides. Score 0.504 Round 2: 273 peptides, 38 chains. Longest chain 23 peptides. Score 0.579 Round 3: 278 peptides, 35 chains. Longest chain 21 peptides. Score 0.625 Round 4: 278 peptides, 37 chains. Longest chain 25 peptides. Score 0.603 Round 5: 280 peptides, 42 chains. Longest chain 18 peptides. Score 0.550 Taking the results from Round 3 Chains 36, Residues 243, Estimated correctness of the model 47.6 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 7883 reflections ( 99.82 % complete ) and 7801 restraints for refining 3505 atoms. 6828 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1993 (Rfree = 0.000) for 3505 atoms. Found 16 (28 requested) and removed 17 (15 requested) atoms. Cycle 22: After refmac, R = 0.1953 (Rfree = 0.000) for 3498 atoms. Found 15 (28 requested) and removed 15 (15 requested) atoms. Cycle 23: After refmac, R = 0.1964 (Rfree = 0.000) for 3494 atoms. Found 18 (28 requested) and removed 17 (15 requested) atoms. Cycle 24: After refmac, R = 0.1960 (Rfree = 0.000) for 3493 atoms. Found 11 (28 requested) and removed 16 (15 requested) atoms. Cycle 25: After refmac, R = 0.1924 (Rfree = 0.000) for 3486 atoms. Found 12 (28 requested) and removed 16 (15 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.08 3.34 Search for helices and strands: 0 residues in 0 chains, 3592 seeds are put forward NCS extension: 24 residues added (1 deleted due to clashes), 3616 seeds are put forward Round 1: 236 peptides, 39 chains. Longest chain 21 peptides. Score 0.459 Round 2: 287 peptides, 40 chains. Longest chain 21 peptides. Score 0.592 Round 3: 287 peptides, 38 chains. Longest chain 22 peptides. Score 0.614 Round 4: 296 peptides, 37 chains. Longest chain 27 peptides. Score 0.646 Round 5: 279 peptides, 36 chains. Longest chain 25 peptides. Score 0.616 Taking the results from Round 4 Chains 42, Residues 259, Estimated correctness of the model 52.9 % 4 chains (50 residues) have been docked in sequence ------------------------------------------------------ 7883 reflections ( 99.82 % complete ) and 7344 restraints for refining 3506 atoms. 6166 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2092 (Rfree = 0.000) for 3506 atoms. Found 25 (28 requested) and removed 30 (15 requested) atoms. Cycle 27: After refmac, R = 0.1948 (Rfree = 0.000) for 3494 atoms. Found 9 (28 requested) and removed 15 (15 requested) atoms. Cycle 28: After refmac, R = 0.1914 (Rfree = 0.000) for 3485 atoms. Found 6 (28 requested) and removed 17 (15 requested) atoms. Cycle 29: After refmac, R = 0.1942 (Rfree = 0.000) for 3469 atoms. Found 17 (28 requested) and removed 15 (15 requested) atoms. Cycle 30: After refmac, R = 0.2126 (Rfree = 0.000) for 3464 atoms. Found 27 (28 requested) and removed 19 (15 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.07 3.33 Search for helices and strands: 0 residues in 0 chains, 3605 seeds are put forward NCS extension: 28 residues added (4 deleted due to clashes), 3633 seeds are put forward Round 1: 246 peptides, 41 chains. Longest chain 14 peptides. Score 0.463 Round 2: 268 peptides, 37 chains. Longest chain 21 peptides. Score 0.577 Round 3: 267 peptides, 33 chains. Longest chain 29 peptides. Score 0.620 Round 4: 266 peptides, 34 chains. Longest chain 19 peptides. Score 0.606 Round 5: 270 peptides, 38 chains. Longest chain 23 peptides. Score 0.571 Taking the results from Round 3 Chains 34, Residues 234, Estimated correctness of the model 46.3 % 2 chains (24 residues) have been docked in sequence ------------------------------------------------------ 7883 reflections ( 99.82 % complete ) and 7696 restraints for refining 3506 atoms. 6706 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2062 (Rfree = 0.000) for 3506 atoms. Found 27 (28 requested) and removed 17 (15 requested) atoms. Cycle 32: After refmac, R = 0.1992 (Rfree = 0.000) for 3514 atoms. Found 15 (28 requested) and removed 17 (15 requested) atoms. Cycle 33: After refmac, R = 0.1952 (Rfree = 0.000) for 3509 atoms. Found 15 (28 requested) and removed 18 (15 requested) atoms. Cycle 34: After refmac, R = 0.1930 (Rfree = 0.000) for 3500 atoms. Found 16 (28 requested) and removed 17 (15 requested) atoms. Cycle 35: After refmac, R = 0.2142 (Rfree = 0.000) for 3495 atoms. Found 28 (28 requested) and removed 18 (15 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.06 3.32 Search for helices and strands: 0 residues in 0 chains, 3615 seeds are put forward NCS extension: 29 residues added (3 deleted due to clashes), 3644 seeds are put forward Round 1: 223 peptides, 42 chains. Longest chain 12 peptides. Score 0.374 Round 2: 246 peptides, 36 chains. Longest chain 17 peptides. Score 0.529 Round 3: 250 peptides, 36 chains. Longest chain 22 peptides. Score 0.540 Round 4: 245 peptides, 36 chains. Longest chain 30 peptides. Score 0.526 Round 5: 241 peptides, 36 chains. Longest chain 20 peptides. Score 0.514 Taking the results from Round 3 Chains 36, Residues 214, Estimated correctness of the model 23.9 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7883 reflections ( 99.82 % complete ) and 8102 restraints for refining 3505 atoms. 7282 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1915 (Rfree = 0.000) for 3505 atoms. Found 18 (28 requested) and removed 17 (15 requested) atoms. Cycle 37: After refmac, R = 0.1866 (Rfree = 0.000) for 3501 atoms. Found 13 (28 requested) and removed 15 (15 requested) atoms. Cycle 38: After refmac, R = 0.1826 (Rfree = 0.000) for 3496 atoms. Found 14 (28 requested) and removed 15 (15 requested) atoms. Cycle 39: After refmac, R = 0.1786 (Rfree = 0.000) for 3490 atoms. Found 13 (28 requested) and removed 15 (15 requested) atoms. Cycle 40: After refmac, R = 0.1739 (Rfree = 0.000) for 3487 atoms. Found 10 (28 requested) and removed 16 (15 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.06 3.32 Search for helices and strands: 0 residues in 0 chains, 3582 seeds are put forward NCS extension: 31 residues added (3 deleted due to clashes), 3613 seeds are put forward Round 1: 200 peptides, 33 chains. Longest chain 14 peptides. Score 0.426 Round 2: 236 peptides, 34 chains. Longest chain 22 peptides. Score 0.525 Round 3: 251 peptides, 33 chains. Longest chain 28 peptides. Score 0.579 Round 4: 251 peptides, 37 chains. Longest chain 20 peptides. Score 0.530 Round 5: 239 peptides, 36 chains. Longest chain 15 peptides. Score 0.508 Taking the results from Round 3 Chains 35, Residues 218, Estimated correctness of the model 35.3 % 2 chains (18 residues) have been docked in sequence ------------------------------------------------------ 7883 reflections ( 99.82 % complete ) and 7698 restraints for refining 3506 atoms. 6794 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1844 (Rfree = 0.000) for 3506 atoms. Found 19 (28 requested) and removed 18 (15 requested) atoms. Cycle 42: After refmac, R = 0.1732 (Rfree = 0.000) for 3503 atoms. Found 12 (28 requested) and removed 17 (15 requested) atoms. Cycle 43: After refmac, R = 0.1701 (Rfree = 0.000) for 3496 atoms. Found 8 (28 requested) and removed 16 (15 requested) atoms. Cycle 44: After refmac, R = 0.1647 (Rfree = 0.000) for 3486 atoms. Found 7 (28 requested) and removed 15 (15 requested) atoms. Cycle 45: After refmac, R = 0.1629 (Rfree = 0.000) for 3476 atoms. Found 4 (28 requested) and removed 15 (15 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.07 3.33 Search for helices and strands: 0 residues in 0 chains, 3570 seeds are put forward NCS extension: 18 residues added (2 deleted due to clashes), 3588 seeds are put forward Round 1: 224 peptides, 42 chains. Longest chain 13 peptides. Score 0.377 Round 2: 250 peptides, 37 chains. Longest chain 19 peptides. Score 0.527 Round 3: 248 peptides, 36 chains. Longest chain 19 peptides. Score 0.534 Round 4: 253 peptides, 35 chains. Longest chain 19 peptides. Score 0.561 Round 5: 234 peptides, 33 chains. Longest chain 16 peptides. Score 0.532 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 35, Residues 218, Estimated correctness of the model 30.1 % 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. 7883 reflections ( 99.82 % complete ) and 7867 restraints for refining 3506 atoms. 7030 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1797 (Rfree = 0.000) for 3506 atoms. Found 0 (28 requested) and removed 12 (15 requested) atoms. Cycle 47: After refmac, R = 0.1768 (Rfree = 0.000) for 3490 atoms. Found 0 (28 requested) and removed 5 (15 requested) atoms. Cycle 48: After refmac, R = 0.1741 (Rfree = 0.000) for 3484 atoms. Found 0 (28 requested) and removed 6 (15 requested) atoms. Cycle 49: After refmac, R = 0.1682 (Rfree = 0.000) for 3476 atoms. Found 0 (28 requested) and removed 8 (15 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 01:53:19 GMT 2018 Job finished. TimeTaking 44.3 Used memory is bytes: 4967448