Mon 24 Dec 00:30:05 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 2hi0-3.4-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2hi0-3.4-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2hi0-3.4-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2hi0-3.4-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/2hi0-3.4-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2hi0-3.4-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 00:30:10 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/2hi0-3.4-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2hi0-3.4-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 324 and 0 Target number of residues in the AU: 324 Target solvent content: 0.6232 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: 2hi0-3.4-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: 58.636 38.695 103.583 90.000 98.094 90.000 Input sequence file: 2hi0-3.4-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 3.401 Wilson plot Bfac: 62.91 6602 reflections ( 99.80 % complete ) and 0 restraints for refining 4247 atoms. Observations/parameters ratio is 0.39 ------------------------------------------------------ Starting model: R = 0.3100 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2723 (Rfree = 0.000) for 4247 atoms. Found 32 (32 requested) and removed 40 (16 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.21 3.48 Search for helices and strands: 0 residues in 0 chains, 4337 seeds are put forward NCS extension: 0 residues added, 4337 seeds are put forward Round 1: 207 peptides, 39 chains. Longest chain 17 peptides. Score 0.362 Round 2: 259 peptides, 45 chains. Longest chain 10 peptides. Score 0.450 Round 3: 268 peptides, 40 chains. Longest chain 15 peptides. Score 0.541 Round 4: 269 peptides, 39 chains. Longest chain 19 peptides. Score 0.556 Round 5: 263 peptides, 33 chains. Longest chain 27 peptides. Score 0.610 Taking the results from Round 5 Chains 33, Residues 230, Estimated correctness of the model 31.8 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ 6602 reflections ( 99.80 % complete ) and 7896 restraints for refining 3491 atoms. 6989 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2320 (Rfree = 0.000) for 3491 atoms. Found 16 (26 requested) and removed 33 (13 requested) atoms. Cycle 2: After refmac, R = 0.2173 (Rfree = 0.000) for 3443 atoms. Found 15 (26 requested) and removed 29 (13 requested) atoms. Cycle 3: After refmac, R = 0.2046 (Rfree = 0.000) for 3417 atoms. Found 15 (25 requested) and removed 16 (12 requested) atoms. Cycle 4: After refmac, R = 0.2007 (Rfree = 0.000) for 3407 atoms. Found 13 (25 requested) and removed 17 (12 requested) atoms. Cycle 5: After refmac, R = 0.1679 (Rfree = 0.000) for 3395 atoms. Found 14 (25 requested) and removed 15 (12 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.23 3.50 Search for helices and strands: 0 residues in 0 chains, 3522 seeds are put forward NCS extension: 35 residues added (5 deleted due to clashes), 3557 seeds are put forward Round 1: 222 peptides, 40 chains. Longest chain 20 peptides. Score 0.399 Round 2: 234 peptides, 39 chains. Longest chain 13 peptides. Score 0.453 Round 3: 257 peptides, 39 chains. Longest chain 15 peptides. Score 0.522 Round 4: 259 peptides, 36 chains. Longest chain 21 peptides. Score 0.565 Round 5: 249 peptides, 36 chains. Longest chain 17 peptides. Score 0.537 Taking the results from Round 4 Chains 36, Residues 223, Estimated correctness of the model 16.8 % 2 chains (16 residues) have been docked in sequence ------------------------------------------------------ 6602 reflections ( 99.80 % complete ) and 7813 restraints for refining 3492 atoms. 6900 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 6: After refmac, R = 0.1918 (Rfree = 0.000) for 3492 atoms. Found 26 (26 requested) and removed 22 (13 requested) atoms. Cycle 7: After refmac, R = 0.1706 (Rfree = 0.000) for 3491 atoms. Found 7 (26 requested) and removed 17 (13 requested) atoms. Cycle 8: After refmac, R = 0.1661 (Rfree = 0.000) for 3478 atoms. Found 4 (26 requested) and removed 17 (13 requested) atoms. Cycle 9: After refmac, R = 0.1722 (Rfree = 0.000) for 3462 atoms. Found 7 (26 requested) and removed 17 (13 requested) atoms. Cycle 10: After refmac, R = 0.1757 (Rfree = 0.000) for 3450 atoms. Found 17 (26 requested) and removed 14 (13 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.18 3.45 Search for helices and strands: 0 residues in 0 chains, 3565 seeds are put forward NCS extension: 20 residues added (0 deleted due to clashes), 3585 seeds are put forward Round 1: 242 peptides, 42 chains. Longest chain 15 peptides. Score 0.437 Round 2: 270 peptides, 41 chains. Longest chain 22 peptides. Score 0.535 Round 3: 275 peptides, 40 chains. Longest chain 14 peptides. Score 0.561 Round 4: 282 peptides, 38 chains. Longest chain 20 peptides. Score 0.602 Round 5: 278 peptides, 37 chains. Longest chain 20 peptides. Score 0.603 Taking the results from Round 5 Chains 37, Residues 241, Estimated correctness of the model 29.6 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6602 reflections ( 99.80 % complete ) and 7872 restraints for refining 3492 atoms. 6945 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 11: After refmac, R = 0.1997 (Rfree = 0.000) for 3492 atoms. Found 24 (26 requested) and removed 18 (13 requested) atoms. Cycle 12: After refmac, R = 0.1804 (Rfree = 0.000) for 3494 atoms. Found 18 (26 requested) and removed 16 (13 requested) atoms. Cycle 13: After refmac, R = 0.1713 (Rfree = 0.000) for 3487 atoms. Found 10 (26 requested) and removed 15 (13 requested) atoms. Cycle 14: After refmac, R = 0.1671 (Rfree = 0.000) for 3478 atoms. Found 16 (26 requested) and removed 16 (13 requested) atoms. Cycle 15: After refmac, R = 0.1616 (Rfree = 0.000) for 3476 atoms. Found 16 (26 requested) and removed 16 (13 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.20 3.47 Search for helices and strands: 0 residues in 0 chains, 3602 seeds are put forward NCS extension: 36 residues added (0 deleted due to clashes), 3638 seeds are put forward Round 1: 231 peptides, 42 chains. Longest chain 13 peptides. Score 0.401 Round 2: 264 peptides, 40 chains. Longest chain 20 peptides. Score 0.530 Round 3: 267 peptides, 36 chains. Longest chain 18 peptides. Score 0.586 Round 4: 265 peptides, 37 chains. Longest chain 19 peptides. Score 0.569 Round 5: 258 peptides, 37 chains. Longest chain 18 peptides. Score 0.550 Taking the results from Round 3 Chains 37, Residues 231, Estimated correctness of the model 24.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 6602 reflections ( 99.80 % complete ) and 7848 restraints for refining 3492 atoms. 6936 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1868 (Rfree = 0.000) for 3492 atoms. Found 25 (26 requested) and removed 14 (13 requested) atoms. Cycle 17: After refmac, R = 0.1740 (Rfree = 0.000) for 3494 atoms. Found 15 (26 requested) and removed 16 (13 requested) atoms. Cycle 18: After refmac, R = 0.1590 (Rfree = 0.000) for 3491 atoms. Found 9 (26 requested) and removed 16 (13 requested) atoms. Cycle 19: After refmac, R = 0.1604 (Rfree = 0.000) for 3479 atoms. Found 14 (26 requested) and removed 14 (13 requested) atoms. Cycle 20: After refmac, R = 0.1462 (Rfree = 0.000) for 3477 atoms. Found 7 (26 requested) and removed 13 (13 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.20 3.47 Search for helices and strands: 0 residues in 0 chains, 3593 seeds are put forward NCS extension: 20 residues added (0 deleted due to clashes), 3613 seeds are put forward Round 1: 236 peptides, 40 chains. Longest chain 15 peptides. Score 0.445 Round 2: 260 peptides, 38 chains. Longest chain 16 peptides. Score 0.543 Round 3: 271 peptides, 42 chains. Longest chain 15 peptides. Score 0.525 Round 4: 278 peptides, 36 chains. Longest chain 35 peptides. Score 0.614 Round 5: 252 peptides, 33 chains. Longest chain 22 peptides. Score 0.582 Taking the results from Round 4 Chains 36, Residues 242, Estimated correctness of the model 33.1 % 1 chains (8 residues) have been docked in sequence ------------------------------------------------------ 6602 reflections ( 99.80 % complete ) and 7680 restraints for refining 3492 atoms. 6720 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1816 (Rfree = 0.000) for 3492 atoms. Found 26 (26 requested) and removed 20 (13 requested) atoms. Cycle 22: After refmac, R = 0.1683 (Rfree = 0.000) for 3486 atoms. Found 5 (26 requested) and removed 14 (13 requested) atoms. Cycle 23: After refmac, R = 0.1674 (Rfree = 0.000) for 3475 atoms. Found 10 (26 requested) and removed 13 (13 requested) atoms. Cycle 24: After refmac, R = 0.1586 (Rfree = 0.000) for 3471 atoms. Found 9 (26 requested) and removed 14 (13 requested) atoms. Cycle 25: After refmac, R = 0.1580 (Rfree = 0.000) for 3464 atoms. Found 10 (26 requested) and removed 14 (13 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.24 3.51 Search for helices and strands: 0 residues in 0 chains, 3600 seeds are put forward NCS extension: 37 residues added (2 deleted due to clashes), 3637 seeds are put forward Round 1: 209 peptides, 34 chains. Longest chain 17 peptides. Score 0.442 Round 2: 231 peptides, 32 chains. Longest chain 22 peptides. Score 0.536 Round 3: 232 peptides, 33 chains. Longest chain 18 peptides. Score 0.526 Round 4: 233 peptides, 30 chains. Longest chain 20 peptides. Score 0.567 Round 5: 225 peptides, 32 chains. Longest chain 18 peptides. Score 0.519 Taking the results from Round 4 Chains 32, Residues 203, Estimated correctness of the model 17.5 % 2 chains (15 residues) have been docked in sequence ------------------------------------------------------ 6602 reflections ( 99.80 % complete ) and 7752 restraints for refining 3492 atoms. 6923 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1804 (Rfree = 0.000) for 3492 atoms. Found 18 (26 requested) and removed 15 (13 requested) atoms. Cycle 27: After refmac, R = 0.1715 (Rfree = 0.000) for 3489 atoms. Found 9 (26 requested) and removed 14 (13 requested) atoms. Cycle 28: After refmac, R = 0.1721 (Rfree = 0.000) for 3483 atoms. Found 4 (26 requested) and removed 15 (13 requested) atoms. Cycle 29: After refmac, R = 0.1684 (Rfree = 0.000) for 3470 atoms. Found 8 (26 requested) and removed 13 (13 requested) atoms. Cycle 30: After refmac, R = 0.1674 (Rfree = 0.000) for 3460 atoms. Found 8 (26 requested) and removed 13 (13 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.24 3.51 Search for helices and strands: 0 residues in 0 chains, 3570 seeds are put forward NCS extension: 20 residues added (0 deleted due to clashes), 3590 seeds are put forward Round 1: 206 peptides, 33 chains. Longest chain 17 peptides. Score 0.446 Round 2: 218 peptides, 29 chains. Longest chain 17 peptides. Score 0.537 Round 3: 240 peptides, 33 chains. Longest chain 18 peptides. Score 0.549 Round 4: 245 peptides, 36 chains. Longest chain 17 peptides. Score 0.526 Round 5: 245 peptides, 36 chains. Longest chain 18 peptides. Score 0.526 Taking the results from Round 3 Chains 33, Residues 207, Estimated correctness of the model 11.1 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6602 reflections ( 99.80 % complete ) and 8016 restraints for refining 3492 atoms. 7221 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1734 (Rfree = 0.000) for 3492 atoms. Found 23 (26 requested) and removed 14 (13 requested) atoms. Cycle 32: After refmac, R = 0.1685 (Rfree = 0.000) for 3499 atoms. Found 15 (26 requested) and removed 14 (13 requested) atoms. Cycle 33: After refmac, R = 0.1664 (Rfree = 0.000) for 3498 atoms. Found 11 (26 requested) and removed 14 (13 requested) atoms. Cycle 34: After refmac, R = 0.1640 (Rfree = 0.000) for 3495 atoms. Found 8 (26 requested) and removed 13 (13 requested) atoms. Cycle 35: After refmac, R = 0.1602 (Rfree = 0.000) for 3487 atoms. Found 7 (26 requested) and removed 13 (13 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.24 3.51 Search for helices and strands: 0 residues in 0 chains, 3606 seeds are put forward NCS extension: 20 residues added (2 deleted due to clashes), 3626 seeds are put forward Round 1: 196 peptides, 34 chains. Longest chain 18 peptides. Score 0.398 Round 2: 217 peptides, 32 chains. Longest chain 18 peptides. Score 0.495 Round 3: 230 peptides, 33 chains. Longest chain 18 peptides. Score 0.520 Round 4: 234 peptides, 34 chains. Longest chain 18 peptides. Score 0.519 Round 5: 219 peptides, 32 chains. Longest chain 17 peptides. Score 0.501 Taking the results from Round 3 Chains 33, Residues 197, Estimated correctness of the model 0.3 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 6602 reflections ( 99.80 % complete ) and 7967 restraints for refining 3492 atoms. 7192 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1714 (Rfree = 0.000) for 3492 atoms. Found 9 (26 requested) and removed 14 (13 requested) atoms. Cycle 37: After refmac, R = 0.1672 (Rfree = 0.000) for 3482 atoms. Found 15 (26 requested) and removed 13 (13 requested) atoms. Cycle 38: After refmac, R = 0.1602 (Rfree = 0.000) for 3482 atoms. Found 8 (26 requested) and removed 14 (13 requested) atoms. Cycle 39: After refmac, R = 0.1567 (Rfree = 0.000) for 3474 atoms. Found 3 (26 requested) and removed 13 (13 requested) atoms. Cycle 40: After refmac, R = 0.1525 (Rfree = 0.000) for 3460 atoms. Found 10 (26 requested) and removed 13 (13 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.22 3.49 Search for helices and strands: 0 residues in 0 chains, 3584 seeds are put forward NCS extension: 26 residues added (1 deleted due to clashes), 3610 seeds are put forward Round 1: 219 peptides, 37 chains. Longest chain 20 peptides. Score 0.432 Round 2: 227 peptides, 33 chains. Longest chain 17 peptides. Score 0.511 Round 3: 232 peptides, 37 chains. Longest chain 20 peptides. Score 0.473 Round 4: 221 peptides, 31 chains. Longest chain 23 peptides. Score 0.520 Round 5: 220 peptides, 33 chains. Longest chain 16 peptides. Score 0.490 Taking the results from Round 4 Chains 31, Residues 190, Estimated correctness of the model 0.3 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6602 reflections ( 99.80 % complete ) and 7993 restraints for refining 3492 atoms. 7264 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1680 (Rfree = 0.000) for 3492 atoms. Found 8 (26 requested) and removed 15 (13 requested) atoms. Cycle 42: After refmac, R = 0.1582 (Rfree = 0.000) for 3482 atoms. Found 12 (26 requested) and removed 13 (13 requested) atoms. Cycle 43: After refmac, R = 0.1516 (Rfree = 0.000) for 3480 atoms. Found 11 (26 requested) and removed 13 (13 requested) atoms. Cycle 44: After refmac, R = 0.1428 (Rfree = 0.000) for 3477 atoms. Found 7 (26 requested) and removed 13 (13 requested) atoms. Cycle 45: After refmac, R = 0.1426 (Rfree = 0.000) for 3469 atoms. Found 10 (26 requested) and removed 13 (13 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.21 3.48 Search for helices and strands: 0 residues in 0 chains, 3574 seeds are put forward NCS extension: 29 residues added (6 deleted due to clashes), 3603 seeds are put forward Round 1: 179 peptides, 31 chains. Longest chain 19 peptides. Score 0.384 Round 2: 201 peptides, 29 chains. Longest chain 20 peptides. Score 0.486 Round 3: 201 peptides, 30 chains. Longest chain 20 peptides. Score 0.472 Round 4: 201 peptides, 28 chains. Longest chain 17 peptides. Score 0.500 Round 5: 196 peptides, 27 chains. Longest chain 20 peptides. Score 0.498 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 28, Residues 173, 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. 6602 reflections ( 99.80 % complete ) and 8211 restraints for refining 3492 atoms. 7547 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1603 (Rfree = 0.000) for 3492 atoms. Found 0 (26 requested) and removed 13 (13 requested) atoms. Cycle 47: After refmac, R = 0.1618 (Rfree = 0.000) for 3477 atoms. Found 0 (26 requested) and removed 5 (13 requested) atoms. Cycle 48: After refmac, R = 0.1565 (Rfree = 0.000) for 3470 atoms. Found 0 (26 requested) and removed 7 (13 requested) atoms. Cycle 49: After refmac, R = 0.1536 (Rfree = 0.000) for 3462 atoms. TimeTaking 43.78